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From: Ahmed S. <ahm...@gm...> - 2018-12-12 09:18:43
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I'm having an issue while trying to view an alignment created by open3dalign through its pymol extension, where it gives me this sort of error over all the molecules in the alignment PyMOL>load /tmp/O3A.25075.mol_dir.Ocbieo/0001.mol2, 0001, 0, mol2 Error: failed to open file "/tmp/O3A.25075.mol_dir.Ocbieo/0001.mol2" I searched through the mailing list and found that somebody had a similar issue but on MacOS, while I'm using Ubuntu 16.04 on the other hand. Your suggestion for him was to re-check if openbabel_for_open3dtools was correctly installed, so I checked again, installed in the open3dtools directory and ran env_bash.sh to make the sure that the path set correctly then I made sure that the path was set to the said directory. I then tried using babel in the commandline to convert an sdf file to mol2, and it converted it but I got these errors *** Open Babel Error in openLib /home/ahmed/open3dtools/bin/plugins/cmlreactformat.so did not load properly. Error: /home/ahmed/open3dtools/bin/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/lib/i386-linux-gnu/libicuuc.so.55) ============================== *** Open Babel Error in openLib /home/ahmed/open3dtools/bin/plugins/cmlformat.so did not load properly. Error: /home/ahmed/open3dtools/bin/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/lib/i386-linux-gnu/libicuuc.so.55) ============================== *** Open Babel Error in openLib /home/ahmed/open3dtools/bin/plugins/pubchem.so did not load properly. Error: /home/ahmed/open3dtools/bin/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/lib/i386-linux-gnu/libicuuc.so.55) ============================== *** Open Babel Error in openLib /home/ahmed/open3dtools/bin/plugins/xmlformat.so did not load properly. Error: /home/ahmed/open3dtools/bin/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/lib/i386-linux-gnu/libicuuc.so.55) ============================== *** Open Babel Error in openLib /home/ahmed/open3dtools/bin/plugins/cdxmlformat.so did not load properly. Error: /home/ahmed/open3dtools/bin/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/lib/i386-linux-gnu/libicuuc.so.55) And pymol still shows the same error when I try to view the alignment. So is there anyway you can help me please? Thanks for your consideration Ahmed Samir |
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From: Paolo T. <pao...@un...> - 2017-06-06 19:10:00
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Hi Ren, can you share test.sdf with me? You don't need to reply to the list - just reply to me. Regards, Paolo On 06/06/17 19:29, Ren Xiaodong wrote: > > Hi: > > > I am trying to use QMD in open3dalign to generate the comformers of a > compound, for further 3d-qsar research. > > > My system is: linux mint 18 64-bit, everything of the open3dalign was > set properly. > > > My procedure are mainly. > > > 1) open3dalign > > > 2）import type=SDF file=test.sdf > > > 3) > > |qmd prm_dir=/home/rxdcpu/00_Program/open3dtools/share/tinker \ > keep_initial=NO \ > minimizer=MINIMIZE \ > min_maxiter=100 \ > min_grad=0.001 \ > rmsd=0.2 \ > range=3.0 \ > temperature=1000 \ > runs=20 \ > window=||5||\ > time_step=1.0 \ > diel_const=1.0 \ > gbsa=NO \ > qmd_dir=qmd_dir \ > remove_qmd_folder=NO| > > > after I enter the above command, it seems the program began running. A > terminal picture is as follow, no any error was found in log file > (it's empty), and all of the cpu were in use. > > but there seems no much output file. the only output file > 0001_000000.out is as follow. > > > > ###################################################################### > ########################################################################## > ### ### > ### TINKER --- Software Tools for Molecular > Design ### > ## ## > ## Version 8.1 February > 2017 ## > ## ## > ## Copyright (c) Jay William Ponder > 1990-2017 ## > ### All Rights > Reserved ### > ### ### > ########################################################################## > ###################################################################### > > > Atoms with an Unusual Number of Attached Atoms : > > Type Atom Name Atom Type Expected Found > > Valence 1-CB 133 3 2 > Valence 2-CB 133 3 2 > Valence 3-CB 133 3 2 > Valence 4-CB 133 3 2 > Valence 5-CB 133 3 2 > > Additional Partial Charges for Specific Atoms : > > Atom Charge > > 1 0.0000 > 2 0.0000 > 3 0.0000 > 4 0.0000 > 5 0.0000 > 6 0.0284 > 7 0.0366 > 8 -0.0650 > 9 -0.0650 > 10 0.6300 > 11 -0.1300 > 12 0.5650 > 13 -0.5000 > 14 -0.5000 > > Limited Memory BFGS Quasi-Newton Optimization : > > QN Iter F Value G RMS F Move X Move Angle FG Call > Comment > > 0 NaN NaN 1 > > > > > Even after it run overnight, The program didn't complete. and no > further output information came out. > > > Can any experienced user tell me what happened? > > > > Best wishes > > Xiaodong > |
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From: Ren X. <rx...@ho...> - 2017-06-06 18:29:33
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Hi:
I am trying to use QMD in open3dalign to generate the comformers of a compound, for further 3d-qsar research.
My system is: linux mint 18 64-bit, everything of the open3dalign was set properly.
My procedure are mainly.
1) open3dalign
2）import type=SDF file=test.sdf
3)
qmd prm_dir=/home/rxdcpu/00_Program/open3dtools/share/tinker \
keep_initial=NO \
minimizer=MINIMIZE \
min_maxiter=100 \
min_grad=0.001 \
rmsd=0.2 \
range=3.0 \
temperature=1000 \
runs=20 \
window=5 \
time_step=1.0 \
diel_const=1.0 \
gbsa=NO \
qmd_dir=qmd_dir \
remove_qmd_folder=NO
after I enter the above command, it seems the program began running. A terminal picture is as follow, no any error was found in log file (it's empty), and all of the cpu were in use.
[cid:247470ef-4e3c-44c9-bdc3-81a9951f14a4]
but there seems no much output file. the only output file 0001_000000.out is as follow.
######################################################################
##########################################################################
### ###
### TINKER --- Software Tools for Molecular Design ###
## ##
## Version 8.1 February 2017 ##
## ##
## Copyright (c) Jay William Ponder 1990-2017 ##
### All Rights Reserved ###
### ###
##########################################################################
######################################################################
Atoms with an Unusual Number of Attached Atoms :
Type Atom Name Atom Type Expected Found
Valence 1-CB 133 3 2
Valence 2-CB 133 3 2
Valence 3-CB 133 3 2
Valence 4-CB 133 3 2
Valence 5-CB 133 3 2
Additional Partial Charges for Specific Atoms :
Atom Charge
1 0.0000
2 0.0000
3 0.0000
4 0.0000
5 0.0000
6 0.0284
7 0.0366
8 -0.0650
9 -0.0650
10 0.6300
11 -0.1300
12 0.5650
13 -0.5000
14 -0.5000
Limited Memory BFGS Quasi-Newton Optimization :
QN Iter F Value G RMS F Move X Move Angle FG Call Comment
0 NaN NaN 1
Even after it run overnight, The program didn't complete. and no further output information came out.
Can any experienced user tell me what happened?
Best wishes
Xiaodong
|
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From: Paolo T. <pao...@un...> - 2016-07-02 21:08:44
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Dear John, when you create a 3D-QSAR model you want to use pIC50 values as dependent variable (-log10 IC50). Greater pIC50 values indicate greater activities. Kind regards, Paolo On 02/07/2016 20:53, John Paul Kowalski wrote: > Hello, another fairly trivial Open 3D QSAR question - I want to make > sure I am understanding the wording of this correctly: > > After importing dependent variable values (IC50 values for example), > when the model is being trained, the default setting (correctly) > assumes that most 'potent' compounds are ones with lowest IC50 values > correct? Or is default where higher dependent variables equate to > higher potency? > > Therefore, when visualizing isocontours, if I set vdw_pos to green > (example from your tutorial) then a green contour that equates to > "steric bulk positively correlating to biological activity" would mean > that steric bulk in this location corresponds to _lower IC50_ and > hence _more potent compound(s)_? > > Apologies if this is spelled out elsewhere on website/tutorial and I > missed it. > > -John Kowalski > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > > > _______________________________________________ > Open3dalign-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dalign-discuss |
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From: John P. K. <ko...@uw...> - 2016-07-02 19:53:30
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Hello, another fairly trivial Open 3D QSAR question - I want to make sure I am understanding the wording of this correctly: After importing dependent variable values (IC50 values for example), when the model is being trained, the default setting (correctly) assumes that most 'potent' compounds are ones with lowest IC50 values correct? Or is default where higher dependent variables equate to higher potency? Therefore, when visualizing isocontours, if I set vdw_pos to green (example from your tutorial) then a green contour that equates to "steric bulk positively correlating to biological activity" would mean that steric bulk in this location corresponds to *lower IC50* and hence *more potent compound(s)*? Apologies if this is spelled out elsewhere on website/tutorial and I missed it. -John Kowalski |
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From: Paolo T. <pao...@un...> - 2016-06-03 08:01:55
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Dear John, you will need to add hydrogens and generate 3D coordinates for your 2D molecule before feeding it into Open3DALIGN. You may conveniently do that with obabel: obabel -i sdf 2d.sdf -o sdf -O 3d.sdf -h --gen3D See attached for input and output files. Cheers, p. On 03/06/16 00:05, John Paul Kowalski wrote: > Hello Dr. Tosco and Open3D community - I recently started using the > Open 3D Align + QSAR pre-built binary distribution for Windows. I am > having an issue with the "qmd" command, I think my problem may be due > to MMFF94 geometry minimization during the iterative procedure that > "qmd" runs through. I have attempted to specify prm_dir parameter to > the folder where |mmff.prm/mmffs.prm| resides as well as simply run > "qmd" on default. > > _The issue is that the .sdf file that is generated depicts hydrocarbon > chains (for all conformations) as completely linear, without the > 'kink' that we would expect for a minimized geometry. Therefore, it > appears I am not generating force field based minimized structures._ > > Am I incorrectly running "qmd" / is there a possible issue with the > windows pre-built / an issue with the Tinker files? > > See attached images of a 2D structure that I imported (before running > "qmd"), and the linear hydrocarbon result after running "qmd" (where > FF optimization did not appear to occur). > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > > > _______________________________________________ > Open3dalign-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dalign-discuss |
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From: John P. K. <ko...@uw...> - 2016-06-02 23:05:52
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Hello Dr. Tosco and Open3D community - I recently started using the Open 3D Align + QSAR pre-built binary distribution for Windows. I am having an issue with the "qmd" command, I think my problem may be due to MMFF94 geometry minimization during the iterative procedure that "qmd" runs through. I have attempted to specify prm_dir parameter to the folder where mmff.prm/mmffs.prm resides as well as simply run "qmd" on default. *The issue is that the .sdf file that is generated depicts hydrocarbon chains (for all conformations) as completely linear, without the 'kink' that we would expect for a minimized geometry. Therefore, it appears I am not generating force field based minimized structures.* Am I incorrectly running "qmd" / is there a possible issue with the windows pre-built / an issue with the Tinker files? See attached images of a 2D structure that I imported (before running "qmd"), and the linear hydrocarbon result after running "qmd" (where FF optimization did not appear to occur). |
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From: Paolo T. <pao...@un...> - 2016-05-15 17:04:04
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Dear John, the best format to import your file is SDF. qmd stores conformations for each molecule in a separate file. You don't need to combine the files. The align keyword, if you use candidate=MULTI and specify conf_dir, will find the conformational databases for you, provided that you point conf_dir to the folder where the conformations are. This step is not needed if you invoked the qmd command within the same O3A session (see http://open3dalign.sourceforge.net/?Description:Keywords:align). Cheers, p. On 14/05/2016 22:05, John Paul Kowalski wrote: > Hello, I am a graduate student in Medicinal Chemistry at the > University of Washington in Seattle, United States. I have just > started to use this software and am very excited for its possibilities > as the academic setting in which I am in prevents purchase of > commercial software suites that run alignment & QSAR functions. > Admittedly, however, I lack any programming experience and my general > computer skills are sub-par. > > I am emailing to inquire as to whether this discuss list is still > active and whether responses will be replied to regarding Open3DAlign > & Open3DQSAR or if correspondences should be directed elsewhere? > > I may as well post my first software question too - > > What is the best file format to use for importing a file with many > chemical structures (with or without IC50 values for example) for > subsequent energy minimization and alignment? My first attempt of > using qmd on a file with many structures yielded individual files for > each molecule, or should I recombine these files afterwords? > > Thank you, > John Kowalski > > > ------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j > > > _______________________________________________ > Open3dalign-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dalign-discuss |
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From: John P. K. <ko...@uw...> - 2016-05-14 21:27:39
|
Hello, I am a graduate student in Medicinal Chemistry at the University of Washington in Seattle, United States. I have just started to use this software and am very excited for its possibilities as the academic setting in which I am in prevents purchase of commercial software suites that run alignment & QSAR functions. Admittedly, however, I lack any programming experience and my general computer skills are sub-par. I am emailing to inquire as to whether this discuss list is still active and whether responses will be replied to regarding Open3DAlign & Open3DQSAR or if correspondences should be directed elsewhere? I may as well post my first software question too - What is the best file format to use for importing a file with many chemical structures (with or without IC50 values for example) for subsequent energy minimization and alignment? My first attempt of using qmd on a file with many structures yielded individual files for each molecule, or should I recombine these files afterwords? Thank you, John Kowalski |
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From: Floersheim, P. <phi...@no...> - 2011-08-24 10:40:17
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A question of a novice to more experienced users: How do I get a log file from a batch run Open3dalign -i test.inp -o test.out The error message in the file test.out qmd_sar_xxx.inp - Line 3 An error occurred during one or more QMD procedures; please check your input/output/log files. QMD failed. Job finished on Wed Aug 24 11:47:41 2011 Abnormal exit. tells me to look for log files, but there are none, and I have checked ./qmd_sar_xxx . Line 3 is: qmd prm=~/o3a/open3dtools/share/tinker qmd_dir=./qmd_sar_xxx Is there a "verbose" or a "debug" option ? Thanks for your kind help, Dr. Philipp Floersheim Novartis Pharma AG Postfach CH-4002 Basel SWITZERLAND Phone +41 61 3245173 Fax +41 61 3242686 phi...@no...<mailto:phi...@no...> www.novartis.com<http://www.novartis.com/> ________________________________ _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. |
