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

Re: [rDock-list-def] Population failure - not enough diversity?

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

Dear Parker,

We have been trying to reproduce the error you are getting, but we have not
succeeded.
Have you identified which molecule is giving this error?
Could you please send the prm, receptor and ligand files? (Or, at least,
the prm and ligand files?)
The more information we can get, the easiest it will be for us to try to
solve this uncommon error.
Thank you!
Best,

Sergio





2014-06-24 23:56 GMT+02:00 Parker de Waal <Par...@va...>:

> Hello,
>
> Recently I've been developing and training a HTVS campaign using the NCI
> Diversity set IV as a test set. However when I went to upscale to the full
> NCI DTP dataset containing ~270,000 compounds I am greeted with the
> following error:
>
> RBT_DOCKING_ERROR at ../src/lib/RbtPopulation.cxx, line 81
> Population failure - not enough diversity
>
> my input is as follows using SF3:
>
> numb=1
> for file in ../../compound_screens/SCREEN_NAME/split*sd; do
>         rbdock -i $file -o docking/first_run/$numb -r receptor.prm -p
> dock.prm -n 10 &
>         numb=$((numb + 1))
>         sleep 20
> done
>
> For my input sdf I used openbabel to protonate and generate 3D coordinates
> before splitting for docking.
>
> If anyone could help I would greatly appreciate it.
>
> Best,
> Parker
>
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[rDock-list-def] Population failure - not enough diversity?

[Parker de W. <Par...@va...>]

Hello,

Recently I've been developing and training a HTVS campaign using the NCI Diversity set IV as a test set. However when I went to upscale to the full NCI DTP dataset containing ~270,000 compounds I am greeted with the following error:

RBT_DOCKING_ERROR at ../src/lib/RbtPopulation.cxx, line 81
Population failure - not enough diversity

my input is as follows using SF3:

numb=1
for file in ../../compound_screens/SCREEN_NAME/split*sd; do
        rbdock -i $file -o docking/first_run/$numb -r receptor.prm -p dock.prm -n 10 &
        numb=$((numb + 1))
        sleep 20
done

For my input sdf I used openbabel to protonate and generate 3D coordinates before splitting for docking.

If anyone could help I would greatly appreciate it.

Best,
Parker

Re: [rDock-list-def] Visualizing cavities

[Szilveszter J. <szi...@gm...>]

I prefer pymol, and isomesh works like dream, thank you!
Cheers:
Szilva

On Wed, May 14, 2014 at 4:24 PM, Sergio Ruiz Carmona
<sru...@gm...> wrote:
> Hi Szilva,
>
> We have never used the rDock GUI, so I can't help you in this aspect.
> What we do for viewing a cavity is to generate a grid with "-d" flag when
> running rbcavity and open it with pymol, for instance.
> A typical command would look like this:
>
>> rbcavity -was -d -r PRMFILE.prm
>
>
> That will generate two files: PRMFILE.as and PRMFILE_cav1.grd.
> Then, what we do is to open in pymol the receptor and the generated grd file
> and create a mesh (isovalue of 0.99) with the grid data as follows:
>
>> isomesh cavity, PRMFILE_cav1, 0.99
>
>
> Hope it helps!
> Sergio Ruiz
>
> PS: Thanks Marko for your reply!
>
>
> 2014-05-14 15:45 GMT+02:00 Szilveszter Juhos <szi...@gm...>:
>>
>> Hi All,
>>
>> Is there an easy way of visualizing the cavities (*.as) crated by
>> rbcavity? Tried to run the rDock GUI from the York webpage but got
>> only NPE when trying to run.
>>
>> Cheers:
>> Szilva
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.
>> Get unparalleled scalability from the best Selenium testing platform
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>
>

Re: [rDock-list-def] Visualizing cavities

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

Hi Szilva,

We have never used the rDock GUI, so I can't help you in this aspect.
What we do for viewing a cavity is to generate a grid with "-d" flag when
running rbcavity and open it with pymol, for instance.
A typical command would look like this:

rbcavity -was -d -r PRMFILE.prm


That will generate two files: *PRMFILE.as* and *PRMFILE_cav1.grd*.
Then, what we do is to open in pymol the receptor and the generated grd
file and create a mesh (isovalue of 0.99) with the grid data as follows:

isomesh cavity, PRMFILE_cav1, 0.99


Hope it helps!
Sergio Ruiz

PS: Thanks Marko for your reply!


2014-05-14 15:45 GMT+02:00 Szilveszter Juhos <szi...@gm...>:

> Hi All,
>
> Is there an easy way of visualizing the cavities (*.as) crated by
> rbcavity? Tried to run the rDock GUI from the York webpage but got
> only NPE when trying to run.
>
> Cheers:
> Szilva
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
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> available
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>

Re: [rDock-list-def] Visualizing cavities

[Marko K. <gen...@gm...>]

Hi Szilva,

I think you can only visualize the .grd files outputted by rbcavity with
'-d' flag, not the distance grid stored is .as files. The former seem to
open natively with InsightII, but for a free alternative, personally, I'm
quite happy with what Chimera displays with the help of a small script one
of the developers made in response to a request related to yours. Check out:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-February/009646.html

Marko


On Wed, May 14, 2014 at 3:45 PM, Szilveszter Juhos
<szi...@gm...>wrote:

> Hi All,
>
> Is there an easy way of visualizing the cavities (*.as) crated by
> rbcavity? Tried to run the rDock GUI from the York webpage but got
> only NPE when trying to run.
>
> Cheers:
> Szilva
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.
> Get unparalleled scalability from the best Selenium testing platform
> available
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] Visualizing cavities

[Szilveszter J. <szi...@gm...>]

Hi All,

Is there an easy way of visualizing the cavities (*.as) crated by
rbcavity? Tried to run the rDock GUI from the York webpage but got
only NPE when trying to run.

Cheers:
Szilva

Re: [rDock-list-def] rDock compilation

[Daniel Á. G. <alg...@gm...>]

Dear Elnaz,

your problem is that the ligand you are using as reference to define the
cavity in the RNA molecule is originally placed many angstroms apart. To
define a cavity using a ligand, the ligand must be inside the cavity you
want to define.

Solution: either manually displace the ligand (using pymol for instance)
inside the binding region, even the pose is not correct, and use these new
coordinates for defining the cavity; or use the Two spheres method to
define the cavity (method that does not require any reference ligand).

To send messages to the rdock-mailing list, you have to subscribe first.
Messages from subscribers do not need a filter and are posted directly to
all the community.

Hope this helps!

Daniel



2014-05-11 13:49 GMT+02:00 elnaz mehdizadeh aghdam <ema...@ya...>:

> Dear Daniel
>
> First I should say that I sent this question to mailing list but it is being
> held until the list moderator can review it for approval. Becuse I do not
> know how much time it took I had to sent the question for you too. I am
> sorry for taking your time.
>
>
> "Dear All
> I've started to dock some RNAs with rDock. First I detach a ligand and RNA
> of a PDB file and docked them again. It maked me glad because the RMSD was
> very low and it seems rDock is a convenient program. However, when I
> started to dock my own RNAs, I came across to a strange problem. My sd
> docked files in pymol showd me that the ligand and receptor are apart from
> each other! I attached the .prm .mol2 and .sd files. It would be great if
> somebody could help."
>
>
>
> Best Regards
> Dr Elnaz Mehdizadeh Aghdam
> PharmD, PhD Student of Pharmaceutical Biotechnology
> Faculty of Pharmacy
> Tabriz University of Medical Sciences
> Tabriz
> Iran.
> Tel: +98 (411) 3372250-239
>
>
>


-- 
Daniel Álvarez | PhD Student
dan...@ub...  | www.ub.edu/cbdd
Computational Biology and Drug Discovery Group
Faculty of Pharmacy | University of Barcelona

Re: [rDock-list-def] What are the changes from 2006.2 version?

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

Dear Kevin,

Indeed, there is no any major change between 2006 and 2013 versions, as you
noted.

The differences between the two versions are the following:
- Now it has been publish and released as open-source software.
- It has been validated against two reference docking programs (Glide and
Vina) for Virtual Screening and Binding Mode Prediction.
- Dependencies on proprietary software (Daylight) have been changed for
free alternatives (OpenBabel) in order to calculate RMSD in a more accurate
way and to run tethered docking.

Best regards,

Sergio Ruiz


2014-05-08 18:13 GMT+02:00 Janghyun Lee <jan...@um...>:

> Hi,
>
> I have been using rDock version 2006.2 before you released the 2013
> version. Did you make any changes from 2006.2 version to 2013 version?
>
> I recently changed the cluster and installed the 2013 version. I have the
> data that was generated by rDock 2006.2, and I need to continue the further
> docking studies using the data. Can I use the version 2013 to continue
> docking to the data? or are there any significant changes to the version
> 2013 that I need to re-start the study?
>
> I saw that the old settings that I used in the 2006.2 are compatible with
> the 2013 version. I could not find a huge discrepancy in terms of scripts
> between 2006.2 version and 2013, but I just want to double-check whether I
> am correct.
>
> Sincerely,
> Kevin
>
>
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>
>

[rDock-list-def] What are the changes from 2006.2 version?

[Janghyun L. <jan...@um...>]

Hi,

I have been using rDock version 2006.2 before you released the 2013
version. Did you make any changes from 2006.2 version to 2013 version?

I recently changed the cluster and installed the 2013 version. I have the
data that was generated by rDock 2006.2, and I need to continue the further
docking studies using the data. Can I use the version 2013 to continue
docking to the data? or are there any significant changes to the version
2013 that I need to re-start the study?

I saw that the old settings that I used in the 2006.2 are compatible with
the 2013 version. I could not find a huge discrepancy in terms of scripts
between 2006.2 version and 2013, but I just want to double-check whether I
am correct.

Sincerely,
Kevin

Re: [rDock-list-def] Compilling rDock_2013_1 on a cluster

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

Hi all,
We have made a short tutorial in rDock webpage regarding this issue.

http://rdock.sourceforge.net/how-to-run-rdock-in-parallel/

At this moment, MPI is not implemented in rDock. As Szilveszter suggested,
it is easier to use a job-scheduler (there is an example in the tutorial).
Best,
Sergio



2014-04-30 11:23 GMT+02:00 Szilveszter Juhos <szi...@gm...>:

> Hi, it is just hundred times easier to use a job-scheduler like Condor
> / LSF / GridEngine instead of implementing the MPI stuff into rDock.
> If you have a cluster, you can have Condor for free, it is relatively
> easy to install/use.
>
> Cheers:
> Szilva
>
> On Wed, Apr 30, 2014 at 10:10 AM, Jose Manuel Gally
> <jos...@un...> wrote:
> > Hi!
> >
> > I would like to know if it's possible to compile a mpi version of rDock
> in
> > order to run it on a cluster?
> > If so could someone explain to me how to do it or redirect me to the
> > relevant documentation?
> >
> > I couldn't find any mpi flag in the make files, or any documentation
> about
> > parallel installation in the pdf guides in $RBT_ROOT/docs.
> >
> > Complementary informations :
> > - The openmpi version on the cluster is 1.6.5 (x64).
> > - I am not an expert in unix environment.
> > - I have the rDock_2013_1 version.
> > - I am running on Centos 6.5 x64.
> > - I could compile rDock without any apparent problem on my local computer
> > following the Getting_Started guide.
> >
> > Thank you for your help!
> >
> > Best regards,
> > Jose Manuel
> >
> >
> > -
> >
> >
> ------------------------------------------------------------------------------
> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> > Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> > unparalleled scalability from the best Selenium testing platform
> available.
> > Simple to use. Nothing to install. Get started now for free."
> > http://p.sf.net/sfu/SauceLabs
> > _______________________________________________
> > rDock-list-def mailing list
> > rDo...@li...
> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def
> >
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
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>

Re: [rDock-list-def] Compilling rDock_2013_1 on a cluster

[Szilveszter J. <szi...@gm...>]

Hi, it is just hundred times easier to use a job-scheduler like Condor
/ LSF / GridEngine instead of implementing the MPI stuff into rDock.
If you have a cluster, you can have Condor for free, it is relatively
easy to install/use.

Cheers:
Szilva

On Wed, Apr 30, 2014 at 10:10 AM, Jose Manuel Gally
<jos...@un...> wrote:
> Hi!
>
> I would like to know if it's possible to compile a mpi version of rDock in
> order to run it on a cluster?
> If so could someone explain to me how to do it or redirect me to the
> relevant documentation?
>
> I couldn't find any mpi flag in the make files, or any documentation about
> parallel installation in the pdf guides in $RBT_ROOT/docs.
>
> Complementary informations :
> - The openmpi version on the cluster is 1.6.5 (x64).
> - I am not an expert in unix environment.
> - I have the rDock_2013_1 version.
> - I am running on Centos 6.5 x64.
> - I could compile rDock without any apparent problem on my local computer
> following the Getting_Started guide.
>
> Thank you for your help!
>
> Best regards,
> Jose Manuel
>
>
> -
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] Compilling rDock_2013_1 on a cluster

[Jose M. G. <jos...@un...>]

Hi!

I would like to know if it's possible to compile a mpi version of rDock 
in order to run it on a cluster?
If so could someone explain to me how to do it or redirect me to the 
relevant documentation?

I couldn't find any mpi flag in the make files, or any documentation 
about parallel installation in the pdf guides in $RBT_ROOT/docs.

Complementary informations :
- The openmpi version on the cluster is 1.6.5 (x64).
- I am not an expert in unix environment.
- I have the rDock_2013_1 version.
- I am running on Centos 6.5 x64.
- I could compile rDock without any apparent problem on my local 
computer following the Getting_Started guide.

Thank you for your help!

Best regards,
Jose Manuel


-

[Rdock-list-def] Fwd: rDock execution error

[Daniel Á. G. <alg...@gm...>]

I forward this question sent to my private email for the record.
Elnaz was missing LD_LIBRARY_PATH declaration pointing to rDock
installation LIB subdirectory as described in last paragraph of
installation page http://rdock.sourceforge.net/installation/

Daniel

---------- Forwarded message ----------
From: <ema...@us...>
Date: 2014-04-20 9:46 GMT+02:00
Subject: rDock
To: d-a...@us...
Cc: ema...@us...

Hi, I build the rDock on ubuntu 13.10 2 days ago successfully. But I could
not run it !
mehdizadeh@mehdizadeh-All-Series:~/Documents/rDock/rDock_2013.1_src$
./bin/rbcavity
./bin/rbcavity: error while loading shared libraries:
libRbt.so.rDock_2013.1_src: cannot open shared object file: No such file or
directory

could you please help me or tell me How can I get information.

Regards
Elnaz Aghdam
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