opengrowth-discuss Mailing List for OpenGrowth (Page 2)
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From: Nicolas C. <nic...@gm...> - 2018-06-29 15:14:07
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Hi, For bindingbox_size, starting with 2 (which will put the initial fragment in a 4*4*4 Angstrom^3 box) seems reasonable. You may have to perform a little trial/error if you don't like the ligands for some reason. Regarding the description of the keywords, if the user manual is not clear enough I can update it. Here are some explanations: * rotation_precision: it is how many times the rotation is performed for new fragments or new starting fragments. For example, in Figure 2 and 3 of the manual, you can count 12 rotamers. * optimization_mode: the user manual says: "Here two parameters are given in one: the first digit describes when the geometry optimization is done, the second digit describes when the optimization as a whole is done. Note that the geometry optimization is performed first to relax the structures. The options for the digits are: 0=no optimization is made; 1=an optimization is made once a ligand has finished growing; 2=an optimization is made after that each best rotamer has been found, 3=an optimization is made for each rotamer. For example, “12” means that the geometry of the ligand will be optimized when it has finished growing (i.e. when it has reached one of the thresholds) and the optimization as a whole will be done after each best rotamer has been found. A value of 22 is usually a good compromise." I don't recommand using 3 (for either first or second digit), it is too much time-consuming and you probably want to first perform the rotamer search. 22 means that once the best rotamer has been found, the geometry will be optimized (first digit) and then the "optimization as a whole" is done (second digit) as in Figure 13. If you want more details let me know. The default parameters should be good for most ligands, they don't really depend on the size of the ligands. The most important parameters are those related to geometry optimization which is the bottleneck in term of speed of the program. It is performed by OpenBabel and I don't have a lot of control on it to optimize it. If you find that the program doesn't grow enough ligands, you can play with them. Best, Nicolas Le ven. 29 juin 2018 à 11:35, ABRUSAN Gyorgy <Gyo...@ig...> a écrit : > Hi Nicolas, > > > Thank you, the first mail was sent without registering to the list, I > thought you didn't receive it. > > > Is there a bindingbox_size value that you have good experiences with? For > example if one deals with ligands of 30-60 heavy atoms, could one say that > a box size parameter of 1 or 2 will perform reasonably well in most cases > (assuming ligands with "typical" topology/complexity)? > > > There are several parameters in the complete *.inp file that are difficult > to interpret for the average user. (like rotation_precision, > optimization_mode, and many others.) Are these parameter combinations > suitable for most ligands (of a reasonable size like 30-60 heavy atoms), > or at least some of them should be adjusted to the expected size of the > new/grown ligand? > > > Best wishes, > > Gyorgy > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenGrowth-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/opengrowth-discuss > |
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From: ABRUSAN G. <Gyo...@ig...> - 2018-06-29 09:35:54
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The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
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From: Nicolas C. <nic...@gm...> - 2018-06-29 07:19:48
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Hi, No need to send your email twice. You can check if your email was send to the mailing list from here: https://sourceforge.net/p/opengrowth/mailman/opengrowth-discuss/ For your question on the size of the binding box: we didn't perform extensive test on that point. If your binding site is large, you can choose a large box size. Since there is a repulsion term in the scoring function, you will not have overlap with the protein and there is no reason this doesn't work. However, you might end up with ligands that start at the border of the binding site and grow in vacuum/the solvent region. Which proportion, I don't know, this needs to be tested (any feedback will be appreciated). Another option is to perform several growth from different parts of the binding site/anchoring points. From a start anywhere in the binding site, theoretically you can still fill the pocket. I would try both (say for 10 000 ligands each) and compare the results (what does the best 100 ligands for each look like). Also, please note that from our experience, if you perform a full de novo growth, you should dock the "best" ligands with an usual docking program (Dock, AutoDock, etc) to check that the pose found by OpenGrowth is realisitic. This is less needed when performing growth from a seed, but still recommanded. Performing the growth from a seed is also recommended when possible to restrict a little bit the chemical space. Nicolas Le jeu. 28 juin 2018 à 19:57, ABRUSAN Gyorgy <Gyo...@ig...> a écrit : > Dear Dr Cheron, > > I would like to ask for some advice on the usage of OpenGrowth. It is a > really neat little tool, and I simply would like to ask for some advice on > parameter settings. How does the "right" setting for the bindingbox size > parameter depends on ligand/binding site size? Basically I would like > OpenGrowth to "explore" the entire binding pocket, but there seems to be no > obvious way of defining the size of the pocket (like in Dock for example), > only its center. I didn't really play with the other parameters, I wonder > whether they are relatively "optimal" for generic use (perhaps with the > exception of the max number of heavy(?) atoms). > > I would greatly appreciate any help or suggestion with this issue. > > Best wishes, > Gyorgy Abrusan > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenGrowth-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/opengrowth-discuss > |
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From: ABRUSAN G. <Gyo...@ig...> - 2018-06-28 17:57:28
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The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
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From: ABRUSAN G. <Gyo...@ig...> - 2018-06-27 16:05:11
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The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
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From: Nicolas C. <nic...@gm...> - 2018-03-28 09:49:32
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Hello, If the example worked, then it means that the problem is not coming from the program or the libraries. So, the problem is coming from your input files. How did you prepare your protein? Is it complete (no missing atoms, no missing residues, hydrogen added)? If not, there will be a problem with the force field. Also, are you sure that the coordinates of the binding site are correct (easy way to check: add a He atom at this position in your protein file, open it with VMD/Chimera/SomethingElse and check that He is at the right place). Nicolas 2018-03-27 15:34 GMT+02:00 我 <wx...@12...>: > Dear Nicolas, > The example works (without changing anything). > But in my own job, the program created 100 ligands, each with an error "Could > not setup force field", and without any output file except a summary file. > The program was run on Linuxmint 17.3 in VirtualBox. The already compiled > OpenGrowth.exe in the downloaded binaries was directly used (one solution > listed in the manual). OpenBabel was obtained from repositories, and > libopenbabel installed according to the manual. > Thank you for your help. > With regards, > Xiaoan Wen > > -- > 温小安 > 中国药科大学药物科学研究院新药研究中心 > 江苏省代谢性疾病药物重点实验室 > 手机：181-0159-8299 > --------------------------------------------------------- > Xiaoan Wen, Ph.D (Med. Chem) > China Pharmaceutical University Center for Drug Discovery > Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases > Nanjing 210009, China > Email: wx...@12... > Mobile Phone: +86 181 0159 8299 <+86%20181%200159%208299> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenGrowth-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/opengrowth-discuss > > |
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From: 我 <wx...@12...> - 2018-03-27 13:34:25
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Dear Nicolas, The example works (without changing anything). But in my own job, the program created 100 ligands, each with an error "Could not setup force field", and without any output file except a summary file. The program was run on Linuxmint 17.3 in VirtualBox. The already compiled OpenGrowth.exe in the downloaded binaries was directly used (one solution listed in the manual). OpenBabel was obtained from repositories, and libopenbabel installed according to the manual. Thank you for your help. With regards, Xiaoan Wen -- 温小安 中国药科大学药物科学研究院新药研究中心 江苏省代谢性疾病药物重点实验室 手机：181-0159-8299 --------------------------------------------------------- Xiaoan Wen, Ph.D (Med. Chem) China Pharmaceutical University Center for Drug Discovery Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases Nanjing 210009, China Email: wx...@12... Mobile Phone: +86 181 0159 8299 |
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From: Nicolas C. <nic...@gm...> - 2018-03-27 09:49:11
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Hi, Please ask your questions to the mailing list and not to me (eventhough I am the person who will answer). Did the example work (without changing anything)? >From your copy/paste, it says it is the 99th ligand: did the program created 98 ligands before? Also, I need more details: which linux distribution, did you compile OpenGrowth, did you compile OpenBabel? Thank you Nicolas 2018-03-26 7:22 GMT+02:00 我 <wx...@12...>: > Hi Nicolas, > > The previous problem has been solved. Thank you very much. > > Yet another problem was given in running my own project. > For each ligand, it was said "Could not setup force field", as follow: > ==== Ligand 99 ==== > ERROR: Could not setup force field. > Fragment 1: Pyrrolidine > Energy: -4.40758 > As results, no ligand files were genarated in output folder. > > I just modified CONFORMERS and BINDING_SITE_X/Y/Z parameters in the > example .inp file according to my own project. > Apart from this, there was no any other change in the .inp file. > > With regard, > > Xiaoan Wen > > > -- > 温小安 > 中国药科大学药物科学研究院新药研究中心 > 江苏省代谢性疾病药物重点实验室 > 手机：181-0159-8299 > --------------------------------------------------------- > Xiaoan Wen, Ph.D (Med. Chem) > China Pharmaceutical University Center for Drug Discovery > Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases > Nanjing 210009, China > Email: wx...@12... > Mobile Phone: +86 181 0159 8299 <+86%20181%200159%208299> > > At 2018-03-23 16:12:36, "Nicolas Cheron" <nic...@gm...> > wrote: > > Hello, > > Thank you for your interest in the program. I think the error is > self-explicit: ERROR: The only possible options for SCORING_FUNCTION are > SMOG2001 or SMOG2016. > > In your output, you can read "The scoring function is: > SMOG2015". You must change it to SMOG2016. > > Best, > > Nicolas > > > > > 2018-03-22 5:56 GMT+01:00 我 <wx...@12...>: > >> Dear Sir/Madam, >> I am learning how to use OpenGrowth. When I followed "Example of use", >> no output folder was created. An error message was given at the end of the >> following information. Would you please guide to resolve the problem? >> >> wxagj-VirtualBox Resources_1.0.1 # ./OpenGrowth.exe >> Input-OpenGrowth-Complete.inp >> ************************************************************************ >> *************** OpenGrowth ************** >> *************** v1.0 ************** >> ************************************************************************ >> *************** Author: Nicolas Chéron ************** >> *************** Eugene Shakhnovich Group ************** >> *************** Harvard CCB, 2015-2017 ************** >> *************** License: GNU GPL v3 ************** >> ************************************************************************ >> *************** Please cite: ************** >> * J. Med. Chem. 2016, pp 4171-4188, DOI: 10.1021/acs.jmedchem.5b00886 * >> * J. Chem. Inf. Model. 2017, pp 584-593, DOI: 10.1021/acs.jcim.6b00610 * >> ************************************************************************ >> >> *********** Start reading the parameter file >> Input-OpenGrowth-Complete.inp ************ >> The conformer name is: >> Structure/2AQU-A_XRay_0.pdb >> Number of conformers to be used: 1 >> The rotamer name is: >> Structure/... >> The protein range is: 20 >> The scoring function is: SMOG2015 >> The energetic parameters will be read from the file: >> KBP-3.5-4.5-10.5.dat >> The X binding site is: 61.9395 >> The Y binding site is: 94.3025 >> The Z binding site is: 27.8725 >> The binding box size is: 0.5 >> The program mode is: DENOVO >> The growth mode is: FOG >> The ligand name is: ... >> The regrow file is: ... >> The branching probability is: 0.5 >> The Monte Carlo temperature is: 1.3 >> The fragment list file is: >> Fragments-OpenGrowth-113/Fragments.dat >> The first fragment probability file is: >> Fragments-OpenGrowth-113/Proba_FirstFrag.dat >> The transition probability file is: >> Fragments-OpenGrowth-113/Proba_Transition.dat >> The vdW scale parameter for inter steric clashes is: 0.7 >> The vdW scale parameter for intra steric clashes is: 0.65 >> The rotation precision is: 24 >> The mode for optimization is: 22 >> The number of optimization iterations is: 20 >> The number of optimization per iteration is: 10 >> The step for translation is: 0.02 >> The angle for rotation is: 0.5 >> The force field used for optimization is: MMFF94 >> The number of steepest descent steps performed is: 5 >> The number of conjugate gradient steps performed is: 0 >> The cut-off for vdW interactions is: 6 >> The cut-off for electrostatic interactions is: 10 >> The maximum number of fragments is: 10 >> The maximum number of heavy atoms is: 60 >> The growth will stop at a molecular weight of: 450 g/mol >> The maximum number of iterations is: 10 >> The minimum number of fragments is: 0 >> The minimum number of heavy atoms is: 0 >> The minimum energy is (we keep struct. with a lower score): 0 >> The output files will be called: >> "Output/Ligand" >> The parameter for writing only SMILES string is: 0 >> The parameter for writing the ligand description is: 0 >> The 3Mer-Screen file is: >> Fragments-OpenGrowth-113/unfound_3mers.dat >> The type of average is: ARITHMETIC >> We will grow: 10 ligand(s) >> The verbose level is: 2 >> No parameter found for the number of rotamers (ROTAMERS_NUMBER). We will >> not use them. >> ERROR: The only possible options for SCORING_FUNCTION are SMOG2001 or >> SMOG2016. >> >> >> >> >> -- >> 温小安 >> 中国药科大学药物科学研究院新药研究中心 >> 江苏省代谢性疾病药物重点实验室 >> 手机：181-0159-8299 >> --------------------------------------------------------- >> Xiaoan Wen, Ph.D (Med. Chem) >> China Pharmaceutical University Center for Drug Discovery >> Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases >> Nanjing 210009, China >> Email: wx...@12... >> Mobile Phone: +86 181 0159 8299 <+86%20181%200159%208299> >> >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> OpenGrowth-discuss mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/opengrowth-discuss >> >> > > > > |
|
From: Nicolas C. <nic...@gm...> - 2018-03-23 08:13:33
|
Hello,
Thank you for your interest in the program. I think the error is
self-explicit: ERROR: The only possible options for SCORING_FUNCTION are
SMOG2001 or SMOG2016.
In your output, you can read "The scoring function is:
SMOG2015". You must change it to SMOG2016.
Best,
Nicolas
2018-03-22 5:56 GMT+01:00 我 <wx...@12...>:
> Dear Sir/Madam,
> I am learning how to use OpenGrowth. When I followed "Example of use", no
> output folder was created. An error message was given at the end of the
> following information. Would you please guide to resolve the problem?
>
> wxagj-VirtualBox Resources_1.0.1 # ./OpenGrowth.exe
> Input-OpenGrowth-Complete.inp
> ************************************************************************
> *************** OpenGrowth **************
> *************** v1.0 **************
> ************************************************************************
> *************** Author: Nicolas Chéron **************
> *************** Eugene Shakhnovich Group **************
> *************** Harvard CCB, 2015-2017 **************
> *************** License: GNU GPL v3 **************
> ************************************************************************
> *************** Please cite: **************
> * J. Med. Chem. 2016, pp 4171-4188, DOI: 10.1021/acs.jmedchem.5b00886 *
> * J. Chem. Inf. Model. 2017, pp 584-593, DOI: 10.1021/acs.jcim.6b00610 *
> ************************************************************************
>
> *********** Start reading the parameter file
> Input-OpenGrowth-Complete.inp ************
> The conformer name is:
> Structure/2AQU-A_XRay_0.pdb
> Number of conformers to be used: 1
> The rotamer name is: Structure/...
> The protein range is: 20
> The scoring function is: SMOG2015
> The energetic parameters will be read from the file:
> KBP-3.5-4.5-10.5.dat
> The X binding site is: 61.9395
> The Y binding site is: 94.3025
> The Z binding site is: 27.8725
> The binding box size is: 0.5
> The program mode is: DENOVO
> The growth mode is: FOG
> The ligand name is: ...
> The regrow file is: ...
> The branching probability is: 0.5
> The Monte Carlo temperature is: 1.3
> The fragment list file is:
> Fragments-OpenGrowth-113/Fragments.dat
> The first fragment probability file is:
> Fragments-OpenGrowth-113/Proba_FirstFrag.dat
> The transition probability file is:
> Fragments-OpenGrowth-113/Proba_Transition.dat
> The vdW scale parameter for inter steric clashes is: 0.7
> The vdW scale parameter for intra steric clashes is: 0.65
> The rotation precision is: 24
> The mode for optimization is: 22
> The number of optimization iterations is: 20
> The number of optimization per iteration is: 10
> The step for translation is: 0.02
> The angle for rotation is: 0.5
> The force field used for optimization is: MMFF94
> The number of steepest descent steps performed is: 5
> The number of conjugate gradient steps performed is: 0
> The cut-off for vdW interactions is: 6
> The cut-off for electrostatic interactions is: 10
> The maximum number of fragments is: 10
> The maximum number of heavy atoms is: 60
> The growth will stop at a molecular weight of: 450 g/mol
> The maximum number of iterations is: 10
> The minimum number of fragments is: 0
> The minimum number of heavy atoms is: 0
> The minimum energy is (we keep struct. with a lower score): 0
> The output files will be called:
> "Output/Ligand"
> The parameter for writing only SMILES string is: 0
> The parameter for writing the ligand description is: 0
> The 3Mer-Screen file is:
> Fragments-OpenGrowth-113/unfound_3mers.dat
> The type of average is: ARITHMETIC
> We will grow: 10 ligand(s)
> The verbose level is: 2
> No parameter found for the number of rotamers (ROTAMERS_NUMBER). We will
> not use them.
> ERROR: The only possible options for SCORING_FUNCTION are SMOG2001 or
> SMOG2016.
>
>
>
>
> --
> 温小安
> 中国药科大学药物科学研究院新药研究中心
> 江苏省代谢性疾病药物重点实验室
> 手机：181-0159-8299
> ---------------------------------------------------------
> Xiaoan Wen, Ph.D (Med. Chem)
> China Pharmaceutical University Center for Drug Discovery
> Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases
> Nanjing 210009, China
> Email: wx...@12...
> Mobile Phone: +86 181 0159 8299 <+86%20181%200159%208299>
>
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenGrowth-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/opengrowth-discuss
>
>
|
|
From: 我 <wx...@12...> - 2018-03-22 04:57:02
|
Dear Sir/Madam, I am learning how to use OpenGrowth. When I followed "Example of use", no output folder was created. An error message was given at the end of the following information. Would you please guide to resolve the problem? wxagj-VirtualBox Resources_1.0.1 # ./OpenGrowth.exe Input-OpenGrowth-Complete.inp ************************************************************************ *************** OpenGrowth ************** *************** v1.0 ************** ************************************************************************ *************** Author: Nicolas Chéron ************** *************** Eugene Shakhnovich Group ************** *************** Harvard CCB, 2015-2017 ************** *************** License: GNU GPL v3 ************** ************************************************************************ *************** Please cite: ************** * J. Med. Chem. 2016, pp 4171-4188, DOI: 10.1021/acs.jmedchem.5b00886 * * J. Chem. Inf. Model. 2017, pp 584-593, DOI: 10.1021/acs.jcim.6b00610 * ************************************************************************ *********** Start reading the parameter file Input-OpenGrowth-Complete.inp ************ The conformer name is: Structure/2AQU-A_XRay_0.pdb Number of conformers to be used: 1 The rotamer name is: Structure/... The protein range is: 20 The scoring function is: SMOG2015 The energetic parameters will be read from the file: KBP-3.5-4.5-10.5.dat The X binding site is: 61.9395 The Y binding site is: 94.3025 The Z binding site is: 27.8725 The binding box size is: 0.5 The program mode is: DENOVO The growth mode is: FOG The ligand name is: ... The regrow file is: ... The branching probability is: 0.5 The Monte Carlo temperature is: 1.3 The fragment list file is: Fragments-OpenGrowth-113/Fragments.dat The first fragment probability file is: Fragments-OpenGrowth-113/Proba_FirstFrag.dat The transition probability file is: Fragments-OpenGrowth-113/Proba_Transition.dat The vdW scale parameter for inter steric clashes is: 0.7 The vdW scale parameter for intra steric clashes is: 0.65 The rotation precision is: 24 The mode for optimization is: 22 The number of optimization iterations is: 20 The number of optimization per iteration is: 10 The step for translation is: 0.02 The angle for rotation is: 0.5 The force field used for optimization is: MMFF94 The number of steepest descent steps performed is: 5 The number of conjugate gradient steps performed is: 0 The cut-off for vdW interactions is: 6 The cut-off for electrostatic interactions is: 10 The maximum number of fragments is: 10 The maximum number of heavy atoms is: 60 The growth will stop at a molecular weight of: 450 g/mol The maximum number of iterations is: 10 The minimum number of fragments is: 0 The minimum number of heavy atoms is: 0 The minimum energy is (we keep struct. with a lower score): 0 The output files will be called: "Output/Ligand" The parameter for writing only SMILES string is: 0 The parameter for writing the ligand description is: 0 The 3Mer-Screen file is: Fragments-OpenGrowth-113/unfound_3mers.dat The type of average is: ARITHMETIC We will grow: 10 ligand(s) The verbose level is: 2 No parameter found for the number of rotamers (ROTAMERS_NUMBER). We will not use them. ERROR: The only possible options for SCORING_FUNCTION are SMOG2001 or SMOG2016. -- 温小安 中国药科大学药物科学研究院新药研究中心 江苏省代谢性疾病药物重点实验室 手机：181-0159-8299 --------------------------------------------------------- Xiaoan Wen, Ph.D (Med. Chem) China Pharmaceutical University Center for Drug Discovery Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases Nanjing 210009, China Email: wx...@12... Mobile Phone: +86 181 0159 8299 |
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From: Muhammad.Ismail <Muh...@bu...> - 2018-01-04 11:17:21
|
Hello prof. Cheron,
I tired to use it with OpenBabel 2.4.1 and it worked. Thank you so much for your support.
Muhammad Ismail
________________________________
From: Nicolas Cheron <nic...@gm...>
Sent: Thursday, January 4, 2018 10:17:09 AM
To: ope...@li...; Muhammad.Ismail
Subject: Re: [OpenGrowth] OpenGrowth compilation problem - Ubuntu 17.10
Hello,
Thank you for your interest in OpenGrowth. I have not yet tried the last development version of OpenBabel and thus can't provide support for it. Do you have the same problem when you are using OpenBabel 2.4.1? If not, I encourage you to use OpenBabel v2.4.1 for which OpenGrowth 1.0 was tested. If yes, then the problem is coming from somewhere else and I will guide you to find it.
Sincerely,
Nicolas Chéron
2018-01-02 17:38 GMT+01:00 Muhammad.Ismail <Muh...@bu...<mailto:Muh...@bu...>>:
Dear all,
I have a problem compiling OpenGrowth on Ubuntu 17.10.
I have compiled the latest OpenBabel version (2.4.90) from Git repositories. Then I went to the “Source” folder -inside the "OpenGrowth_1.0" unzipped folder- and edited the Makefile file according to my needs and typed "make", the following error appeared:
Energy_SMOG2001.cpp:22:22: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsNotCorH’
if (nbr->IsNotCorH()) { polarity++; }
^~~~~~~~~
Energy_SMOG2001.cpp:27:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsHydrogen’; did you mean ‘IsPolarHydrogen’?
if (atom->IsHydrogen()) { atomType = "H"; }
^~~~~~~~~~
IsPolarHydrogen
Energy_SMOG2001.cpp:28:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsSulfur’
else if (atom->IsSulfur() || atom->IsPhosphorus()) { atomType = "SL"; }
^~~~~~~~
Energy_SMOG2001.cpp:28:44: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsPhosphorus’
else if (atom->IsSulfur() || atom->IsPhosphorus()) { atomType = "SL"; }
^~~~~~~~~~~~
Energy_SMOG2001.cpp:30:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsNitrogen() && (atom->GetValence() > atom->GetHyb()) ) { atomType = "NC"; } // A nitrogen is charged if its valence is higher than its hybridation
^~~~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:31:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsNitrogen() && atom->IsHbondDonor()) { atomType = "ND"; }
^~~~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:32:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsNitrogen() && atom->IsHbondAcceptor()) { atomType = "NA"; }
^~~~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:34:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsOxygen() && atom->MatchesSMARTS("[O;$(O=*)]")) { atomType = "OB"; }
^~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:35:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsOxygen() && atom->IsHbondAcceptor()) { atomType = "OA"; }
^~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:36:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsOxygen() && atom->IsHbondDonor()) { atomType = "OD"; }
^~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:37:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && (atom->GetHyb()==3) && polarity==0) { atomType = "C3"; }
^~~~~~~~
Energy_SMOG2001.cpp:38:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && (atom->GetHyb()==2) && polarity==0) { atomType = "C2"; }
^~~~~~~~
Energy_SMOG2001.cpp:39:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && (atom->GetHyb()==1) && polarity==0) { atomType = "C2"; }
^~~~~~~~
Energy_SMOG2001.cpp:40:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && atom->MatchesSMARTS("[#6;$(C=O)]")) { atomType = "CC"; }
^~~~~~~~
Energy_SMOG2001.cpp:41:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && atom->MatchesSMARTS("[#6;$(C(=N)(N)(N))]")) { atomType = "CC"; }
^~~~~~~~
Energy_SMOG2001.cpp:42:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && polarity!=0) { atomType = "CP"; }
^~~~~~~~
Makefile:48: recipe for target 'Energy_SMOG2001.o' failed
make: *** [Energy_SMOG2001.o] Error 1
Thanks for your guidance.
Muhammad Ismail
------------------------------------------------------------------------------
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|
From: Nicolas C. <nic...@gm...> - 2018-01-04 08:17:59
|
Hello,
Thank you for your interest in OpenGrowth. I have not yet tried the last
development version of OpenBabel and thus can't provide support for it. Do
you have the same problem when you are using OpenBabel 2.4.1? If not, I
encourage you to use OpenBabel v2.4.1 for which OpenGrowth 1.0 was tested.
If yes, then the problem is coming from somewhere else and I will guide you
to find it.
Sincerely,
Nicolas Chéron
2018-01-02 17:38 GMT+01:00 Muhammad.Ismail <Muh...@bu...>:
> Dear all,
>
>
> I have a problem compiling OpenGrowth on Ubuntu 17.10.
>
>
> I have compiled the latest OpenBabel version (2.4.90) from Git
> repositories. Then I went to the “Source” folder -inside the
> "OpenGrowth_1.0" unzipped folder- and edited the Makefile file according to
> my needs and typed "make", the following error appeared:
>
>
> Energy_SMOG2001.cpp:22:22: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsNotCorH’
> if (nbr->IsNotCorH()) { polarity++; }
> ^~~~~~~~~
> Energy_SMOG2001.cpp:27:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsHydrogen’; did you mean ‘IsPolarHydrogen’?
> if (atom->IsHydrogen())
> { atomType = "H"; }
> ^~~~~~~~~~
> IsPolarHydrogen
> Energy_SMOG2001.cpp:28:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsSulfur’
> else if (atom->IsSulfur() || atom->IsPhosphorus())
> { atomType = "SL"; }
> ^~~~~~~~
> Energy_SMOG2001.cpp:28:44: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsPhosphorus’
> else if (atom->IsSulfur() || atom->IsPhosphorus())
> { atomType = "SL"; }
> ^~~~~~~~~~~~
> Energy_SMOG2001.cpp:30:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
> else if (atom->IsNitrogen() && (atom->GetValence() >
> atom->GetHyb()) ) { atomType = "NC"; } // A nitrogen is
> charged if its valence is higher than its hybridation
> ^~~~~~~~~~
> IsNitroOxygen
> Energy_SMOG2001.cpp:31:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
> else if (atom->IsNitrogen() && atom->IsHbondDonor())
> { atomType = "ND"; }
> ^~~~~~~~~~
> IsNitroOxygen
> Energy_SMOG2001.cpp:32:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
> else if (atom->IsNitrogen() && atom->IsHbondAcceptor())
> { atomType = "NA"; }
> ^~~~~~~~~~
> IsNitroOxygen
> Energy_SMOG2001.cpp:34:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
> else if (atom->IsOxygen() && atom->MatchesSMARTS("[O;$(O=*)]"))
> { atomType = "OB"; }
> ^~~~~~~~
> IsNitroOxygen
> Energy_SMOG2001.cpp:35:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
> else if (atom->IsOxygen() && atom->IsHbondAcceptor())
> { atomType = "OA"; }
> ^~~~~~~~
> IsNitroOxygen
> Energy_SMOG2001.cpp:36:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
> else if (atom->IsOxygen() && atom->IsHbondDonor())
> { atomType = "OD"; }
> ^~~~~~~~
> IsNitroOxygen
> Energy_SMOG2001.cpp:37:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsCarbon’
> else if (atom->IsCarbon() && (atom->GetHyb()==3) &&
> polarity==0) { atomType = "C3"; }
> ^~~~~~~~
> Energy_SMOG2001.cpp:38:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsCarbon’
> else if (atom->IsCarbon() && (atom->GetHyb()==2) &&
> polarity==0) { atomType = "C2"; }
> ^~~~~~~~
> Energy_SMOG2001.cpp:39:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsCarbon’
> else if (atom->IsCarbon() && (atom->GetHyb()==1) &&
> polarity==0) { atomType = "C2"; }
> ^~~~~~~~
> Energy_SMOG2001.cpp:40:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsCarbon’
> else if (atom->IsCarbon() && atom->MatchesSMARTS("[#6;$(C=O)]"))
> { atomType = "CC"; }
> ^~~~~~~~
> Energy_SMOG2001.cpp:41:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsCarbon’
> else if (atom->IsCarbon() && atom->MatchesSMARTS("[#6;$(C(=N)(N)(N))]"))
> { atomType = "CC"; }
> ^~~~~~~~
> Energy_SMOG2001.cpp:42:24: error: ‘class OpenBabel::OBAtom’ has no member
> named ‘IsCarbon’
> else if (atom->IsCarbon() && polarity!=0)
> { atomType = "CP"; }
> ^~~~~~~~
> Makefile:48: recipe for target 'Energy_SMOG2001.o' failed
> make: *** [Energy_SMOG2001.o] Error 1
>
> Thanks for your guidance.
>
> Muhammad Ismail
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenGrowth-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/opengrowth-discuss
>
>
|
|
From: Muhammad.Ismail <Muh...@bu...> - 2018-01-02 19:12:16
|
Dear all,
I have a problem compiling OpenGrowth on Ubuntu 17.10.
I have compiled the latest OpenBabel version (2.4.90) from Git repositories. Then I went to the “Source” folder -inside the "OpenGrowth_1.0" unzipped folder- and edited the Makefile file according to my needs and typed "make", the following error appeared:
Energy_SMOG2001.cpp:22:22: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsNotCorH’
if (nbr->IsNotCorH()) { polarity++; }
^~~~~~~~~
Energy_SMOG2001.cpp:27:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsHydrogen’; did you mean ‘IsPolarHydrogen’?
if (atom->IsHydrogen()) { atomType = "H"; }
^~~~~~~~~~
IsPolarHydrogen
Energy_SMOG2001.cpp:28:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsSulfur’
else if (atom->IsSulfur() || atom->IsPhosphorus()) { atomType = "SL"; }
^~~~~~~~
Energy_SMOG2001.cpp:28:44: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsPhosphorus’
else if (atom->IsSulfur() || atom->IsPhosphorus()) { atomType = "SL"; }
^~~~~~~~~~~~
Energy_SMOG2001.cpp:30:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsNitrogen() && (atom->GetValence() > atom->GetHyb()) ) { atomType = "NC"; } // A nitrogen is charged if its valence is higher than its hybridation
^~~~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:31:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsNitrogen() && atom->IsHbondDonor()) { atomType = "ND"; }
^~~~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:32:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsNitrogen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsNitrogen() && atom->IsHbondAcceptor()) { atomType = "NA"; }
^~~~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:34:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsOxygen() && atom->MatchesSMARTS("[O;$(O=*)]")) { atomType = "OB"; }
^~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:35:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsOxygen() && atom->IsHbondAcceptor()) { atomType = "OA"; }
^~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:36:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsOxygen’; did you mean ‘IsNitroOxygen’?
else if (atom->IsOxygen() && atom->IsHbondDonor()) { atomType = "OD"; }
^~~~~~~~
IsNitroOxygen
Energy_SMOG2001.cpp:37:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && (atom->GetHyb()==3) && polarity==0) { atomType = "C3"; }
^~~~~~~~
Energy_SMOG2001.cpp:38:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && (atom->GetHyb()==2) && polarity==0) { atomType = "C2"; }
^~~~~~~~
Energy_SMOG2001.cpp:39:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && (atom->GetHyb()==1) && polarity==0) { atomType = "C2"; }
^~~~~~~~
Energy_SMOG2001.cpp:40:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && atom->MatchesSMARTS("[#6;$(C=O)]")) { atomType = "CC"; }
^~~~~~~~
Energy_SMOG2001.cpp:41:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && atom->MatchesSMARTS("[#6;$(C(=N)(N)(N))]")) { atomType = "CC"; }
^~~~~~~~
Energy_SMOG2001.cpp:42:24: error: ‘class OpenBabel::OBAtom’ has no member named ‘IsCarbon’
else if (atom->IsCarbon() && polarity!=0) { atomType = "CP"; }
^~~~~~~~
Makefile:48: recipe for target 'Energy_SMOG2001.o' failed
make: *** [Energy_SMOG2001.o] Error 1
Thanks for your guidance.
Muhammad Ismail
|
|
From: Nicolas C. <nic...@gm...> - 2017-05-03 20:24:39
|
Hello, This is very strange because this function (PrepareFragments) has not changed between v0.43 and v1.0. Did you use exactly the same files (input file and fragments folder) with v0.43 and v1.0? Which version of Resources file did you use? What you can do is the following: * open PrepareFragments.cpp * add between lines 125 and 126: cout << "DEBUG: fragment " << i << ", " << nameValue << "\t" << fragment[i].obMol.NumAtoms() << "\t" << sizeFragment << "\t" << fragment[i].growth.size() << endl; * recompile and re-try. It should display one line for the preparation of each fragment. The three numbers displayed at the end of the line should be equal and if not the program will stop and display the ERROR line you mentioned. Please tell me for which fragment there is a problem. Regarding "MAX_FRAGMENTS" in the input file, it is point 2. See page 15 of the manual : "MAX_FRAGMENTS Will stop the growth if this number of fragments is reached". Nicolas PS : be aware that you are not using the unfound_3mers list of the set of 413 fragments, but the one from the set of 113 fragments. ---------- Forwarded message ---------- > From: Marawan Ahmed <mm...@ua...> > Date: 2017-05-02 21:52 GMT+02:00 > Subject: [OpenGrowth] Opengrowth error > To: ope...@li... > > > Hello, > I am trying to use the new version of OpenGrowth, however, it seems for me > that the new version has some problems in fragments definition, and it > keeps giving me this error: > > ERROR: some of the arrays describing the fragments have not the same size. > > > Which is not happening if i use the same inputs with Opengrowth0.43. > > Here is my input: > ################ > CONFORMERS og_input/receptor_0.pdb > CONFORMERS_NUMBER 1 > BINDING_SITE_X 3.08 > BINDING_SITE_Y 6.09 > BINDING_SITE_Z 13.24 > BINDINGBOX_SIZE 20.0 > GROWTH_MODE FOG > LIGAND og_input/og_xyz_0.xyz > MODE SEED > > > FRAGMENT_LIST Fragments-OpenGrowth-413/Fragments.dat > PROBA_FIRSTFRAG Fragments-OpenGrowth-413/Proba_FirstFrag.dat > PROBA_TRANSITION Fragments-OpenGrowth-413/Proba_Transition.dat > OUTPUT og_output/Ligand > > > ROTATION_PRECISION 24 > OPTIMIZATION_MODE 22 > OPTIMIZATION_NUMBER 20 > OPTIMIZATION_ITERATIONS 10 > OPTIMIZATION_DISTANCE 0.02 > OPTIMIZATION_ANGLE 0.5 > > OPTIMIZATION_FORCEFIELD MMFF94 > OPTIMIZATION_STEEPDESC 25 > OPTIMIZATION_CONJGRAD 5 > OPTIMIZATION_VDWCUTOFF 6.0 > OPTIMIZATION_ELECCUTOFF 8.0 > > > MAX_FRAGMENTS 9 > MAX_ATOMS 60 > MAX_MW 500 > MAX_ITERATIONS 10 > MIN_FRAGMENTS 4 > MIN_ATOMS 0 > MIN_ENERGY 0 > > 3MERSCREEN Fragments-OpenGrowth-113/unfound_3mers.dat > AVERAGE_TYPE ARITHMETIC > NUMBER_OUTPUT 500 > VERBOSE 2 > > > Also, It is not clear from the manual what is the "MAX_FRAGMENTS" really > means. Does it mean this is the: > 1- The maximum number of fragments to be tried simultaneously in one > iteration. > 2- The maximum number of fragments to be joined to the seed structure in > one output. > > We have compiled opengrowth as the binaries are not working on our > machines. > Thanks in advance, > Regards, > Marawan > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenGrowth-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/opengrowth-discuss > > > |
|
From: Marawan A. <mm...@ua...> - 2017-05-02 20:16:16
|
Hello, I am trying to use the new version of OpenGrowth, however, it seems for me that the new version has some problems in fragments definition, and it keeps giving me this error: ERROR: some of the arrays describing the fragments have not the same size. Which is not happening if i use the same inputs with Opengrowth0.43. Here is my input: ################ CONFORMERS og_input/receptor_0.pdb CONFORMERS_NUMBER 1 BINDING_SITE_X 3.08 BINDING_SITE_Y 6.09 BINDING_SITE_Z 13.24 BINDINGBOX_SIZE 20.0 GROWTH_MODE FOG LIGAND og_input/og_xyz_0.xyz MODE SEED FRAGMENT_LIST Fragments-OpenGrowth-413/Fragments.dat PROBA_FIRSTFRAG Fragments-OpenGrowth-413/Proba_FirstFrag.dat PROBA_TRANSITION Fragments-OpenGrowth-413/Proba_Transition.dat OUTPUT og_output/Ligand ROTATION_PRECISION 24 OPTIMIZATION_MODE 22 OPTIMIZATION_NUMBER 20 OPTIMIZATION_ITERATIONS 10 OPTIMIZATION_DISTANCE 0.02 OPTIMIZATION_ANGLE 0.5 OPTIMIZATION_FORCEFIELD MMFF94 OPTIMIZATION_STEEPDESC 25 OPTIMIZATION_CONJGRAD 5 OPTIMIZATION_VDWCUTOFF 6.0 OPTIMIZATION_ELECCUTOFF 8.0 MAX_FRAGMENTS 9 MAX_ATOMS 60 MAX_MW 500 MAX_ITERATIONS 10 MIN_FRAGMENTS 4 MIN_ATOMS 0 MIN_ENERGY 0 3MERSCREEN Fragments-OpenGrowth-113/unfound_3mers.dat AVERAGE_TYPE ARITHMETIC NUMBER_OUTPUT 500 VERBOSE 2 Also, It is not clear from the manual what is the "MAX_FRAGMENTS" really means. Does it mean this is the: 1- The maximum number of fragments to be tried simultaneously in one iteration. 2- The maximum number of fragments to be joined to the seed structure in one output. We have compiled opengrowth as the binaries are not working on our machines. Thanks in advance, Regards, Marawan |
|
From: Nicolas C. <nic...@gm...> - 2017-04-26 18:38:38
|
First test email send at ope...@li... |
