rdock-list-def — General Mailing List for rDock users

[rDock-list-def] Installation troubles

[Iván F. <iva...@gm...>]

Hi, I'm trying to install rDock in my computer and when I try the command
make linux-g++-64, I get the following error:


Makefile.linux-g++-release-lib:558: fallo en las instrucciones para el
objetivo 'linux-g++/release/obj/RbtGPFFCHK1.o'
make[2]: *** [linux-g++/release/obj/RbtGPFFCHK1.o] Error 1
make[2]: *** Se espera a que terminen otras tareas....
Makefile.linux-g++-release-lib:561: fallo en las instrucciones para el
objetivo 'linux-g++/release/obj/RbtGPFFCrossDock.o'
make[2]: *** [linux-g++/release/obj/RbtGPFFCrossDock.o] Error 1
Makefile.linux-g++-release-lib:552: fallo en las instrucciones para el
objetivo 'linux-g++/release/obj/NMSearch.o'
make[2]: *** [linux-g++/release/obj/NMSearch.o] Error 1
Makefile.linux-g++-release-lib:555: fallo en las instrucciones para el
objetivo 'linux-g++/release/obj/RbtGPChromosome.o'
make[2]: *** [linux-g++/release/obj/RbtGPChromosome.o] Error 1
make[2]: se sale del directorio
'/home/ivan/Descargas/dev/rDock_2013.1_src/build'
Makefile:93: fallo en las instrucciones para el objetivo 'rdock-lib'
make[1]: *** [rdock-lib] Error 2
make[1]: se sale del directorio
'/home/ivan/Descargas/dev/rDock_2013.1_src/build'
makefile:70: fallo en las instrucciones para el objetivo 'linux-g++'
make: *** [linux-g++] Error 2

Do you know how to solve it?

Thanks,
Ivan Felsztyna

[rDock-list-def] (no subject)

[Gueye V. <gue...@ya...>]

Hi everyone,I am a new user of rDock software. I am trying to use the pharmacophoric restraint implementation which one if I quite understand allow me to fix those specific coordinate (with specific tolerance) in the docking. But I have several warning 
1) WARNING SetupPartialIonicGroups : Inconsistent subunit names in atom list headed by UNK:GLU_4: NBut I guess this warning just tell me that my pdbfile have some inconsistency but seems not to affect the docking. more important I think, I have this warning:2)**WARNING** RBT_MODEL_ERROR at ../src/lib/RbtMdlFileSource.cxx, line 405015 make too few bonds
I launch my docking and there is no difference between constrained and no constrained one in terms on output.  it seems that the pharmacophoric section is correctly read : RbtPharmaSF: Reading mandatory ph4 constraints from /home/v/Desktop/pharma.restr but not restraint.PRM file: RBT_PARAMETER_FILE_V1.00 TITLE premier
RECEPTOR_FILE /home/v/Desktop/receptor.mol2SECTION MAPPER SITE_MAPPER RbtLigandSiteMapper REF_MOL /home/v/Desktop/ligand.sd  RADIUS 6.0 SMALL_SPHERE 1.0  MIN_VOLUME 100 MAX_CAVITIES 1  VOL_INCR 0.0  GRIDSTEP 0.5END_SECTIONSECTION CAVITY SCORING_FUNCTION RbtCavityGridSF  WEIGHT 1.0END_SECTIONSECTION PHARMA SCORING_FUNCTION RbtPharmaSF WEIGHT 1.0 CONSTRAINTS_FILE /home/v/Desktop/pharma.restrEND_SECTION
pharma.restr file:21.17 0.47 -2.81 0.1 Any22.06 0.01 -1.75 0.1 Hyd21.07 1.79 -2.99 0.1 Hyd
thank you,Veronica 

[rDock-list-def] error at sdrmsd execution

[Céline L. <cel...@in...>]

Hi,

I just installed RDock on ubuntu. I run the test (make test) and it was 
successful.

Then, I tried the validation set (Binding Mode Prediction in Proteins) 
with no problem until the last step.

Here is the error, do you have any idea please ?

> sdrmsd 1sj0_ligand.sd 1sj0_docking_out_sorted.sd
Traceback (most recent call last):
   File "/usr/local/bin/RDock/rDock_2013.1_src//bin/sdrmsd", line 199, in 
<module>
     crystal = next(pybel.readfile("sdf", xtal))
AttributeError: 'module' object has no attribute 'readfile'


Best regards

Céline

-- 
Céline Labbé
INSERM U973 - MTi Bioinformatics
CDithem platform
Université Paris Diderot
Bâtiment Lamarck A
39 rue Hélène Brion
75205 PARIS Cedex 13
tel: 01 57 27 84 35

Re: [rDock-list-def] Has anybody tried to run rDock on a Mac?

[Carlos F. <fae...@gm...>]

Hi all,
I am curious as to whether someone has successfully installed rDock on a Mac
Please let me know
Thank you
Carlos Faerman

[rDock-list-def] Score discrepancies between dock.prm and dock_solv.prm

[Brigit S. <bri...@gm...>]

Hello,

I have been using rDock for the past few months to dock small molecules
against RNA targets. After exploring different parameters to find which one
works best with my model, I noticed a huge difference in scores for the
same docking conformation when using dock.prm or dock_solv.prm.

For a few tests, I arrived at the same docking position with the same
ligand and target, and parameters, but using dock.prm for one, and
dock_solv,prm for the other.

The score component that seems to be causing this discrepancy is the
<SCORE.SYSTEM> section (these differ by around 100 with dock_solv scores
being greater than dock scores), however in the following subsections of
<SCORE.SYSTEM> there is no other difference in scoring that would cause a
huge difference in the overall score.

What contributes the "SCORE.SYSTEM" component and why does it differ when
using the different docking protocols? Which protocol is more accurate for
RNA targets?

Thank you,
Brigit

Re: [rDock-list-def] rDock Instillation Issues

[Sergio R. C. <sru...@gm...>]

Dear Matthew Lovelace,

I have checked and it looks like you have a crossing of processor
architectures.
If your computer is 32 bits, please run "make linux-g++", and if it is 64
bits, run "make linux-g++-64".
Before that, remove everything and start from scratch, as maybe some
initial execution with bad architecture generated incorrect files.

Best,

Sergio Ruiz

2017-06-23 5:21 GMT+02:00 Matt Lovelace <mlo...@gm...>:

> Hi,
>
> I've been having some trouble installing rDock that I hope you can help me
> with.
>
> I've been following the instructions and have installed all the necessary
> prerequisite packages but I'm have having trouble it seems with getting an
> executable form of the program. When I type make linux-g++-64 it seems to
> be running smoothly until the end when it says:
>
>
>  /usr/bin/ld: i386:x86-64 architecture of input file
> `/tmp/mpl0713_2017_06_13_20_21_22_19cb91ff-170a-4a09-bab6-56742808ee78/xalt.o'
> is incompatible with i386 output
>
> /usr/bin/ld: link errors found, deleting executable
> `libRbt.so.rDock_2013.1_src'
>
> collect2: ld returned 1 exit status
>
> make[2]: *** [linux-g++/release/lib/libRbt.so.rDock_2013.1_src] Error 1
> make[2]: Leaving directory `/home1/04770/mpl0713/rDock_2013.1_src/build'
>
> make[1]: *** [rdock-lib] Error 2
> make[1]: Leaving directory `/home1/04770/mpl0713/rDock_2013.1_src/build'
>
> make: *** [linux-g++] Error 2
>
>
> Do you have any suggestions on how to alleviate this problem?
>
> Thanks,
>
> Matthew Lovelace
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>

[rDock-list-def] rDock Instillation Issues

[Matt L. <mlo...@gm...>]

Hi,

I've been having some trouble installing rDock that I hope you can help me
with.

I've been following the instructions and have installed all the necessary
prerequisite packages but I'm have having trouble it seems with getting an
executable form of the program. When I type make linux-g++-64 it seems to
be running smoothly until the end when it says:


 /usr/bin/ld: i386:x86-64 architecture of input file
`/tmp/mpl0713_2017_06_13_20_21_22_19cb91ff-170a-4a09-bab6-56742808ee78/xalt.o'
is incompatible with i386 output

/usr/bin/ld: link errors found, deleting executable
`libRbt.so.rDock_2013.1_src'

collect2: ld returned 1 exit status

make[2]: *** [linux-g++/release/lib/libRbt.so.rDock_2013.1_src] Error 1
make[2]: Leaving directory `/home1/04770/mpl0713/rDock_2013.1_src/build'

make[1]: *** [rdock-lib] Error 2
make[1]: Leaving directory `/home1/04770/mpl0713/rDock_2013.1_src/build'

make: *** [linux-g++] Error 2


Do you have any suggestions on how to alleviate this problem?

Thanks,

Matthew Lovelace

[rDock-list-def] Fwd: population failure error in big datasets

[Sergio R. C. <sru...@gm...>]

---------- Forwarded message ----------
From: Linus Manubens-Gil <lin...@cr...>
Date: 2017-03-06 19:33 GMT+01:00
Subject: Re: [rDock-list-def] population failure error in big datasets
To: Sergio Ruiz Carmona <sru...@gm...>


Dear Sergio,

So simple! Even though I looked at the mesh in pymol I was too newbie to
see that something was wrong.

Thank you very much for your help.

Best,

Linus


On 06/03/17 15:28, Sergio Ruiz Carmona wrote:

Dear Linus,

I have seen a couple of problems with your data:
First of all, when you create the cavity you only need 1 reference ligand
for the REF_MOL field in the prm (you have the same file as the input sdf
files with 17 ligands).
And second, this ligand has to be in the actual binding cavity where you
want to dock the ligands so rbcavity can correctly define it.

In your case, the ligands you used for creating the cavity are in a
different part, so the cavity created and used then for docking is
completely wrong. The "population failure error" then comes as rDock is
placing the ligand in a wrongly defined cavity, as it was docking into
vacuum.

In the tutorial page "Docking in 3 steps"
<http://rdock.sourceforge.net/docking-in-3-steps/> of rDock webpage, you
have a useful section that would have solved your problem, or at least let
you know what was wrong, as by viewing the generated cavity in pymol
highlighted your issue:

With the -d flag a grid “.grd” file is generated. This file can be
visualized in a molecular viewer to check the generated cavity. For
example, in pymol (after loading by: pymol <RECEPTOR>.mol2 <LIGAND>.sd
<GRID>.grd), write the following command in the console:

isomesh cavity, <GRID>.grd, 0.99

Hope that helps!

Best,

Sergio

2017-03-06 14:55 GMT+01:00 Linus Manubens-Gil <lin...@cr...>:

> Hi,
>
> I'm working on a big ligand dataset obtained with various tranches from
> ZINC15.
>
> Similar to the issue Parker de Waal brought up in 2014, I get the
> "Population failure - not enough diversity" error.
> https://sourceforge.net/p/rdock/mailman/message/32502753/
> My problem is that not only a single molecule in the dataset is producing
> the error. I get it from at least one ligand in many sd files.
> Is it possible to run the docking ignoring this error and discarding the
> ligands that produce them?
> Or are these errors indicating I'm missing some preprocessing?
>
> I attach the files needed to reproduce the error. The command lines I used
> for generating the cavity and docking are:
>
> rbcavity -was -d -r dock_trial.prm
>
> and
>
> rbdock -i  AAAAML.xaa.sdf -o test_output -r dock_trial.prm -p dock.prm -n
> 50
>
> Thank you very much for the support,
> Best,
>
> --
> Linus Manubens Gil, PhD student
> Lab 522.04 - Cellular & Systems Neurobiology
> Systems Biology
> Centre for Genomic Regulation (CRG)
> c/Dr. Aiguader 88
> 08003, Barcelona
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>

-- 
Linus Manubens Gil, PhD student
Lab 522.04 - Cellular & Systems Neurobiology
Systems Biology
Centre for Genomic Regulation (CRG)
c/Dr. Aiguader 88
08003, Barcelona

Re: [rDock-list-def] population failure error in big datasets

[Sergio R. C. <sru...@gm...>]

Dear Linus,

I have seen a couple of problems with your data:
First of all, when you create the cavity you only need 1 reference ligand
for the REF_MOL field in the prm (you have the same file as the input sdf
files with 17 ligands).
And second, this ligand has to be in the actual binding cavity where you
want to dock the ligands so rbcavity can correctly define it.

In your case, the ligands you used for creating the cavity are in a
different part, so the cavity created and used then for docking is
completely wrong. The "population failure error" then comes as rDock is
placing the ligand in a wrongly defined cavity, as it was docking into
vacuum.

In the tutorial page "Docking in 3 steps"
<http://rdock.sourceforge.net/docking-in-3-steps/> of rDock webpage, you
have a useful section that would have solved your problem, or at least let
you know what was wrong, as by viewing the generated cavity in pymol
highlighted your issue:

With the -d flag a grid “.grd” file is generated. This file can be
visualized in a molecular viewer to check the generated cavity. For
example, in pymol (after loading by: pymol <RECEPTOR>.mol2 <LIGAND>.sd
<GRID>.grd), write the following command in the console:

isomesh cavity, <GRID>.grd, 0.99

Hope that helps!

Best,

Sergio

2017-03-06 14:55 GMT+01:00 Linus Manubens-Gil <lin...@cr...>:

> Hi,
>
> I'm working on a big ligand dataset obtained with various tranches from
> ZINC15.
>
> Similar to the issue Parker de Waal brought up in 2014, I get the
> "Population failure - not enough diversity" error.
> https://sourceforge.net/p/rdock/mailman/message/32502753/
> My problem is that not only a single molecule in the dataset is producing
> the error. I get it from at least one ligand in many sd files.
> Is it possible to run the docking ignoring this error and discarding the
> ligands that produce them?
> Or are these errors indicating I'm missing some preprocessing?
>
> I attach the files needed to reproduce the error. The command lines I used
> for generating the cavity and docking are:
>
> rbcavity -was -d -r dock_trial.prm
>
> and
>
> rbdock -i  AAAAML.xaa.sdf -o test_output -r dock_trial.prm -p dock.prm -n
> 50
>
> Thank you very much for the support,
> Best,
>
> --
> Linus Manubens Gil, PhD student
> Lab 522.04 - Cellular & Systems Neurobiology
> Systems Biology
> Centre for Genomic Regulation (CRG)
> c/Dr. Aiguader 88
> 08003, Barcelona
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>

[rDock-list-def] population failure error in big datasets

[Linus Manubens-G. <lin...@cr...>]

Hi,

I'm working on a big ligand dataset obtained with various tranches from 
ZINC15.

Similar to the issue Parker de Waal brought up in 2014, I get the 
"Population failure - not enough diversity" error.
https://sourceforge.net/p/rdock/mailman/message/32502753/

My problem is that not only a single molecule in the dataset is 
producing the error. I get it from at least one ligand in many sd files.
Is it possible to run the docking ignoring this error and discarding the 
ligands that produce them?
Or are these errors indicating I'm missing some preprocessing?

I attach the files needed to reproduce the error. The command lines I 
used for generating the cavity and docking are:

rbcavity -was -d -r dock_trial.prm

and

rbdock -i  AAAAML.xaa.sdf -o test_output -r dock_trial.prm -p dock.prm -n 50

Thank you very much for the support,
Best,

-- 
Linus Manubens Gil, PhD student
Lab 522.04 - Cellular & Systems Neurobiology
Systems Biology
Centre for Genomic Regulation (CRG)
c/Dr. Aiguader 88
08003, Barcelona

Re: [rDock-list-def] Installation failure

[Sergio R. C. <sru...@gm...>]

Dear Abdullahi,

Please follow thoroughly the instructions indicated in the website (and in
the INSTALL file from the zipped source code):

http://rdock.sourceforge.net/installation/

The problem I see is that you don't have one of the required libraries
(popt-devel), you need to install it and the rest of dependencies before
proceeding with "make linux-g++-64".
Best,

Sergi

2017-02-13 11:24 GMT+01:00 Abdullahi IU <abd...@gm...>:

> Hi Sergio,
>
> I attached the screen shot of the error message.
>
> Maybe, I missed something.
>
>
> I used ' sudo apt-get install csh' and then downloaded
>
> rDock_2013.1_src.tar.gz
>
> I continued according to the installation instruction.
>
> Best regards,
>
> Abdullah
>
>
> On Mon, Feb 13, 2017 at 12:09 PM, Sergio Ruiz Carmona <
> sru...@gm...> wrote:
>
>> Dear Abdullahi,
>>
>> Could you please provide more details about the error? What is the output
>> of 'make linux-g++-64'?
>> Did you thoroughly follow the instructions and installed all the
>> dependencies?
>> Best,
>>
>> Sergi
>>
>> 2017-02-12 14:27 GMT+01:00 Abdullahi IU <abd...@gm...>:
>>
>>> Hi
>>>
>>> I had problem installing rDOCK on Ubuntu 64 bit despite following the
>>> instruction for installation.
>>>
>>> I got the following error message:
>>> recipe for targer ' linux-g++-64' failed.
>>>
>>> Need your help please
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> rDock-list-def mailing list
>>> rDo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>>>
>>
>>
>

Re: [rDock-list-def] Installation failure

[Sergio R. C. <sru...@gm...>]

Dear Abdullahi,

Could you please provide more details about the error? What is the output
of 'make linux-g++-64'?
Did you thoroughly follow the instructions and installed all the
dependencies?
Best,

Sergi

2017-02-12 14:27 GMT+01:00 Abdullahi IU <abd...@gm...>:

> Hi
>
> I had problem installing rDOCK on Ubuntu 64 bit despite following the
> instruction for installation.
>
> I got the following error message:
> recipe for targer ' linux-g++-64' failed.
>
> Need your help please
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] Installation failure

[Abdullahi IU <abd...@gm...>]

Hi

I had problem installing rDOCK on Ubuntu 64 bit despite following the instruction for installation.

I got the following error message:
recipe for targer ' linux-g++-64' failed.

Need your help please

Re: [rDock-list-def] Comparing docking of multiple molecules

[Sergio R. C. <sru...@gm...>]

Dear James,

This is explained in the User Manual and the rDock publication.
However, your extremely high and positive scores suggest that you did
something wrong with your docking jobs.
The best scores should be negative and in the range of -10 and -40.

Best,

Sergio



2016-11-14 22:59 GMT+01:00 James Johnson <tot...@gm...>:

> Looking at some preliminary results <SCORE> doesn't seem like what I am
> looking for as there are many repeated scores: http://pastebin.com/raw/
> 6ZSsghnK
>
> Which is the correct one?
>
> Thanks.
>
> - Jonathan
>
> On Mon, Nov 14, 2016 at 11:51 AM, James Johnson <tot...@gm...>
> wrote:
>
>> I was wondering what number I should look at to compare the docking
>> scores of each molecule in order to rank them.
>>
>> Is it just the pure <SCORE>?
>>
>> Thank you!
>>
>> - James
>>
>
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>

Re: [rDock-list-def] receptor mol2 needs parameters as well as prm file?

[Sergio R. C. <sru...@gm...>]

Dear James,

Without checking your mol2 file, it is difficult to know exactly what
happened to you.
Normally this kind of errors are related to your specific structure
preparation and mol2 format.
I assume you managed to solve it by supplying a correct mol2 file, with the
corresponding sections.

Best,

Sergi

2016-11-14 20:47 GMT+01:00 James Johnson <tot...@gm...>:

> I tried running rbdock and got a peculiar error: Missing
> RBT_PARAMETER_FILE_V1.00 string in 2drd_without_minocycline.mol2
>
> command prompt output: http://pastebin.com/raw/YFwDdTgk
>
> I thought this was just supposed to be in the prm file. So I added the prm
> lines to the beginning of the receptor mol2 file and everything ran fine.
>
> Is this the intending way of doing the docking, or am I doing something
> wrong?
>
> Thank you!
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>

Re: [rDock-list-def] Comparing docking of multiple molecules

[James J. <tot...@gm...>]

Looking at some preliminary results <SCORE> doesn't seem like what I am
looking for as there are many repeated scores:
http://pastebin.com/raw/6ZSsghnK

Which is the correct one?

Thanks.

- Jonathan

On Mon, Nov 14, 2016 at 11:51 AM, James Johnson <tot...@gm...>
wrote:

> I was wondering what number I should look at to compare the docking scores
> of each molecule in order to rank them.
>
> Is it just the pure <SCORE>?
>
> Thank you!
>
> - James
>

[rDock-list-def] output sdf not same coordinate as receptor's cavity

[James J. <tot...@gm...>]

I noticed that The output sdf does not have the same coordinates as the
receptor's cavity.

I was wondering if there was a way to preserve the docking coordinates so I
can visualize where the molecule is docking exactly?

Thank you!

- James

[rDock-list-def] Ways to improve accuracy of docking?

[James J. <tot...@gm...>]

I was wondering what parameters I could give to improve the accuracy of the
docking?

The only variable I was able to find was the amount of runs per ligand -r.

Are there any parameters that change how each run is ran? (Werid word
choice, but couldn't word it better, haha).

Thank you!

- James

[rDock-list-def] Comparing docking of multiple molecules

[James J. <tot...@gm...>]

I was wondering what number I should look at to compare the docking scores
of each molecule in order to rank them.

Is it just the pure <SCORE>?

Thank you!

- James

[rDock-list-def] sd file format

[James J. <tot...@gm...>]

I was wondering if sd was equivalent to sdf. I ran the docking with sdf and
it ran fine.

Also I was wondering if I needed to add partial charges to the sd/sdf file
before docking.

Thank you!

- James

[rDock-list-def] receptor mol2 needs parameters as well as prm file?

[James J. <tot...@gm...>]

I tried running rbdock and got a peculiar error: Missing
RBT_PARAMETER_FILE_V1.00 string in 2drd_without_minocycline.mol2

command prompt output: http://pastebin.com/raw/YFwDdTgk

I thought this was just supposed to be in the prm file. So I added the prm
lines to the beginning of the receptor mol2 file and everything ran fine.

Is this the intending way of doing the docking, or am I doing something
wrong?

Thank you!

Re: [rDock-list-def] rbcavity Gives Docking Site Total volume 0 A^3

[James J. <tot...@gm...>]

Silly me, I used the wrong coordinates (chimera preserved the atom
coordinates correctly).

Thank you!

- James

On Mon, Nov 14, 2016 at 2:59 AM, Sergio Ruiz Carmona <sru...@gm...
> wrote:

> Dear James,
>
> I have checked your input files and they are correct.
> Have you moved your receptor to a different coordinate space than the one
> in the PDB?
> The problem is that the coordinates you gave for the cavity generation are
> not in the same coordinate system, so that's why you are getting 0 A^3 (all
> the large spheres cover all the possible search zone, as explained in the
> manual).
>
> Best,
>
> Sergio
>
> 2016-11-14 7:15 GMT+01:00 James Johnson <tot...@gm...>:
>
>> The only thing I didn't have was a sd file of the ligand but I was just
>> generating the cavity with the RbtSphereSiteMapper so I figured I didn't
>> need it.
>>
>> The center is at one of the removed minocycline coordinates. I have used
>> this coordinate for other programs (autodock vina) with no problems.
>>
>> command line: http://pastebin.com/raw/ZJ8Jr0dZ
>> test.prm: http://pastebin.com/raw/5Rnc4PTN
>>
>> 2drd_without_minocycline.mol2 was generated from 2drd.pdb with chimera.
>> removed minocycline, added hydrogens, added charges, outputted to mol2.
>>
>> Thanks for the help!
>>
>> - James
>>
>> ------------------------------------------------------------
>> ------------------
>> Developer Access Program for Intel Xeon Phi Processors
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Re: [rDock-list-def] rbcavity Gives Docking Site Total volume 0 A^3

[Sergio R. C. <sru...@gm...>]

Dear James,

I have checked your input files and they are correct.
Have you moved your receptor to a different coordinate space than the one
in the PDB?
The problem is that the coordinates you gave for the cavity generation are
not in the same coordinate system, so that's why you are getting 0 A^3 (all
the large spheres cover all the possible search zone, as explained in the
manual).

Best,

Sergio

2016-11-14 7:15 GMT+01:00 James Johnson <tot...@gm...>:

> The only thing I didn't have was a sd file of the ligand but I was just
> generating the cavity with the RbtSphereSiteMapper so I figured I didn't
> need it.
>
> The center is at one of the removed minocycline coordinates. I have used
> this coordinate for other programs (autodock vina) with no problems.
>
> command line: http://pastebin.com/raw/ZJ8Jr0dZ
> test.prm: http://pastebin.com/raw/5Rnc4PTN
>
> 2drd_without_minocycline.mol2 was generated from 2drd.pdb with chimera.
> removed minocycline, added hydrogens, added charges, outputted to mol2.
>
> Thanks for the help!
>
> - James
>
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> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today. http://sdm.link/xeonphi
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[rDock-list-def] rbcavity Gives Docking Site Total volume 0 A^3

[James J. <tot...@gm...>]

The only thing I didn't have was a sd file of the ligand but I was just
generating the cavity with the RbtSphereSiteMapper so I figured I didn't
need it.

The center is at one of the removed minocycline coordinates. I have used
this coordinate for other programs (autodock vina) with no problems.

command line: http://pastebin.com/raw/ZJ8Jr0dZ
test.prm: http://pastebin.com/raw/5Rnc4PTN

2drd_without_minocycline.mol2 was generated from 2drd.pdb with chimera.
removed minocycline, added hydrogens, added charges, outputted to mol2.

Thanks for the help!

- James

Re: [rDock-list-def] Rotable ligand bonds define

[Sergio R. C. <sru...@gm...>]

Dear Matteo,

I am afraid that you can't define independently each of the bonds as
rotatable or not.
However, there is an interesting feature of rDock that can be useful for
you in this case: the sdtether.
With sdtether you can define a part of a ligand as fixed, and rDock won't
move or rotate any of the atoms that match your defined SMARTS pattern, so
you could actually define a SMARTS with your rotatable bond and the atoms
surrounding and it will remain fixed during docking. Keep in mind that in
this case you should need this part of the ligand to be already present in
the binding site.
You can take a look on the manual to get more details:
http://rdock.sourceforge.net/documentation/

Best,

Sergio

2016-07-08 17:47 GMT+02:00 Matteo Uggeri <m....@ho...>:

> Dear All.
>
>
> Can you tell if is it possible to define which bonds are able to rotate
> (or not) in the ligand during the docking?
>
> If I understand the program use a full flexible ligand, so does it allow
> the double bounds rotation?
>
>
> For example, I'm trying to dock a ligand with an alkene chain and some
> bounds are in a resonance form. I don't want it to rotate.
>
>
> Can you help me?
>
>
> Matteo.
>
>
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