ADL: autodock Digest, Vol 58, Issue 22

Qinghua Liao fantasticqhl at yahoo.com
Fri Jun 19 01:22:17 PDT 2009


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To: autodock at scripps.edu
Sent: Friday, June 19, 2009 3:29:40 PM
Subject: autodock Digest, Vol 58, Issue 22

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Today's Topics:

  1. Re:  another error in energy grid calculation while running
      DOVIS (Kukol, Andreas)
  2. Re:  cluster analysis of different dlg files (Stefano Forli)
  3.  write_lowest_energy_ligand.py (Jack Shultz)
  4.  energy minimization (Ravi Sharma)
  5. Re:  write_lowest_energy_ligand.py (Bagdevi)
  6. Re:  energy minimization (Bagdevi)
  7. Re:  regarding active site (for Davide) (Gnanasekar Gopal)


----------------------------------------------------------------------

Message: 1
Date: Thu, 18 Jun 2009 21:18:32 +0100
From: "Kukol, Andreas" <a.kukol at herts.ac.uk>
Subject: Re: ADL: another error in energy grid calculation while
    running    DOVIS
To: "autodock at scripps.edu" <autodock at scripps.edu>
Message-ID:
    <2F848DC922C8D741BF3A60B7D7108B6A826EF4C431 at UH-MAILSTOR.herts.ac.uk>
Content-Type: text/plain; charset="us-ascii"

I suppose, the path and filename of 'PROJECT_specs1/protein/protein_maps.log' is correct ?

I am not sure about this error. You need to make sure, that ALL program files DOVIS uses are excecutable. They are located in various folders, maybe you missed some.

Best wishes
Andreas

________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of liangzichem [liangzichem at yahoo.com.cn]
Sent: 18 June 2009 09:53
To: autodock
Subject: ADL: another error in energy grid calculation while running DOVIS

Thank you for your suggestion. I changed run permission according to your advices and this proceeding could run correctly. But after that, there was an new error in energy grid calculation and job has stopped again.

The error message is:

$ dovis_dock_main.pl -p PROJECT_specs1

Clean up 'jobs' directory
Creat job_list from ligand_list
input: PROJECT_specs1/parameter/ligand_list
output: PROJECT_specs1/jobs/job_list
block size: 2
/home/lfang/test/TK_random_ligs.sd --> 9 mols
Totoal number of jobs: 5
Computing energy grids ...
Energy grid calculation PID 7469
1 molecule converted
adding gasteiger charges to peptide
sh: PROJECT_specs1/protein/protein_maps.log: No such file or directory
PID 7469 finished
There was an error in energy grid calculation.
STOP!


And the contents of protein_maps.log are:

DOVIS AUTODOCK4 ENERGY GRID CALCULATION
Program started: Thu Jun 18 15:44:40 2009
Read dovis_grid_input
GRID_CENTER 46.600 83.790 54.210
GRID_DIMENSION 22.5 22.5 22.5
GRID_SPACING 0.375
PROTEIN /usr/local/dovis/data/test_data/1kim_protein.pdb
Energy grid points: 60 60 60
Prepare runtime GPF file
Convert protein to mol2 format
babel return value 0
Convert protein to pdbqt format
prepare_receptor4.py return value 0
Compute energy grids

And I found "err code: 6"  in "protein_maps.status" .

Thank you so much for your advices!

My best regards,
Vivian Fang




>Yes, this has to do with the permissions to execute files under Linux. You need to make all DOVIS programs (.py and others) executable for all users, if DOVIS has been installed by root.

Alternatively each user need to install his/her own local copy of DOVIS.

Best wishes
Andreas
________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of liangzichem [liangzichem at yahoo.com.cn]
Sent: 17 June 2009 08:48
To: autodock
Subject: ADL: an error in energy grid calculation while running DOVIS

Hi, all

When I started a DOVIS docking run, there was an error in energy grid calculation and job has stopped.
The error message is:

.../dovis_dock_main.pl -p project_specs
Clean up 'jobs' directory
Creat job_list from ligand_list
Computing energy grids ...
Energy grid calculation PID 720
There was an error in energy grid calculation.
STOP!
PID 720 finished
There was an error in energy grid calculation.
STOP!

Could you please suggest me  any solution?

Thank you very much
Vivian Fang
2009-06-17



2009-06-18



liangzichem
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



------------------------------

Message: 2
Date: Thu, 18 Jun 2009 14:14:01 -0700
From: Stefano Forli <forli at scripps.edu>
Subject: Re: ADL: cluster analysis of different dlg files
To: "autodock at scripps.edu" <autodock at scripps.edu>,
    "emiliawu at dicp.ac.cn"    <emiliawu at dicp.ac.cn>
Message-ID: <4A3AAE19.1060100 at scripps.edu>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

Hi Emilia,

you can cluster many dlg's by copying them in a single directory and using the ADT interface:

Analyze->Dockings->Open all... [to load the files]

Analyze->Clustering->Recluster [to re-cluster them accordingly to given RMS tolerance]

Hope this helps,

Stefano



emiliawu at dicp.ac.cn wrote:
> Hi all,
> 
> Is there any way to do the cluster analysis for different dlg files. I just want to split 200 docking run to different computers to make it faster, but I am wondering how can I get the cluster information after all the jobs done.
> Thanks you very much!
> 
> Emilia
> 
> ___________________________________
> DICP WebMail, http://webmail.dicp.ac.cn
> 
> 
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---


-- 
  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-5
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

    tel: (858) 784-2055
    fax: (858) 784-2860
    email: forli at scripps.edu


------------------------------

Message: 3
Date: Thu, 18 Jun 2009 18:38:50 -0400
From: Jack Shultz <js at drugdiscoveryathome.com>
Subject: ADL: write_lowest_energy_ligand.py
To: autodock at scripps.edu
Message-ID:
    <6c65435e0906181538j9eddd44pd1f167828c4e9398 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

I am wondering if it is possible to derive ligand structures in pdb
format from the docking results. I need to take these ligands an run
further analysis with antechamber. This script produces a structure
that does not seem compatible with antechamber.


write_lowest_energy_ligand.py
setting PYTHONHOME environment
write_lowest_energy_ligand: dlgfilename must be specified.
Usage: write_lowest_energy_ligand.py -f dlgfilename

    Description of command...
        -f    dlgfilename
    Optional parameters:
        [-v]    verbose output
        [-o pdbqt_filename] (output filename)


-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org


------------------------------

Message: 4
Date: Fri, 19 Jun 2009 07:42:40 +0530 (IST)
From: Ravi Sharma <ravi_pharma_biotech at yahoo.co.in>
Subject: ADL: energy minimization
To: autodock at scripps.edu
Message-ID: <917157.55090.qm at web95401.mail.in2.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Energy minimization of? receptor file is required before preparing the receptor file for docking...?

I need to do docking
..
please reply....




Thanks.




      Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com

------------------------------

Message: 5
Date: Fri, 19 Jun 2009 11:47:09 +0530
From: Bagdevi <bagdevi.mishra at gmail.com>
Subject: Re: ADL: write_lowest_energy_ligand.py
To: autodock at scripps.edu
Message-ID:
    <c1a055830906182317k5d1e773cjd753198a7be1b6f6 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Well, this script generates the pdbqt format for the ligand. There is
another script "pdbqt_to_pdb.py" which can be used to convert the
pdbqt to pdb file format.

Regards,
Bagdevi Mishra.




On Fri, Jun 19, 2009 at 4:08 AM, Jack Shultz<js at drugdiscoveryathome.com> wrote:
> I am wondering if it is possible to derive ligand structures in pdb
> format from the docking results. I need to take these ligands an run
> further analysis with antechamber. This script produces a structure
> that does not seem compatible with antechamber.
>
>
> write_lowest_energy_ligand.py
> setting PYTHONHOME environment
> write_lowest_energy_ligand: dlgfilename must be specified.
> Usage: write_lowest_energy_ligand.py -f dlgfilename
>
>    Description of command...
>        -f    dlgfilename
>    Optional parameters:
>        [-v]    verbose output
>        [-o pdbqt_filename] (output filename)
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


------------------------------

Message: 6
Date: Fri, 19 Jun 2009 11:52:19 +0530
From: Bagdevi <bagdevi.mishra at gmail.com>
Subject: Re: ADL: energy minimization
To: autodock at scripps.edu
Message-ID:
    <c1a055830906182322l4df4f03bv62869992dc975f5a at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Energy minimization is not mandatory to perform before docking. But
yes, if you do it, you would get more genuine results.

Regards,
Bagdevi Mishra.




On Fri, Jun 19, 2009 at 7:42 AM, Ravi
Sharma<ravi_pharma_biotech at yahoo.co.in> wrote:
> Energy minimization of  receptor file is required before preparing the receptor file for docking...?
>
> I need to do docking
> ..
> please reply....
>
>
>
>
> Thanks.
>
>
>
>
>      Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


------------------------------

Message: 7
Date: Fri, 19 Jun 2009 00:29:38 -0700 (PDT)
From: Gnanasekar Gopal <ggmacro at yahoo.com>
Subject: Re: ADL: regarding active site (for Davide)
To: autodock at scripps.edu
Message-ID: <547369.12192.qm at web111003.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Dear Davide,

It is not a problem. I think no need to remove your autodock-vina from your computer. You can download the autodock4 software and install in your computer. Before autodock4 downloading, you should install Cygwin software.

Cheers,
G.G




________________________________
From: Davide Mercadante <dmer018 at aucklanduni.ac.nz>
To: autodock at scripps.edu
Sent: Wednesday, June 17, 2009 2:22:44 PM
Subject: Re: ADL: regarding active site

Dear Dr. Oleg Trott,

thanks infintely for your help. I will try using autodock-vina to see if I
am able to solve the problem. I have autodock 4 now installed on my machine.
Should I remove it before installing Autodock-Vina or can I just go through
the installation of autodock-vina without removing autodock4?

Thanks again,

Cheers,
Davide

2009/6/16 Oleg Trott <trott at scripps.edu>

> David,
>
> What problem are you referring to? If it's ligands going far outside
> the search space then, like I just wrote, I don't think it will happen
> in Vina.
>
> Oleg
>
> On Sun, Jun 14, 2009 at 1:30 PM, Davide
> Mercadante<dmer018 at aucklanduni.ac.nz> wrote:
> > Dear Oleg,
> >
> > sorry for the late reply. I am using Autodock 4 and not Autodock Vina.
> So,
> > do you advice me to use Vina?
> >? Do you think I will be able to solve the problem?
> >
> > Cheers,
> > Davide
> >
> > 2009/6/14 Oleg Trott <trott at scripps.edu>
> >
> >> On Fri, Jun 12, 2009 at 3:53 PM, Davide
> >> Mercadante<dmer018 at aucklanduni.ac.nz> wrote:
> >>
> >> > 2) After the calculations the docked ligands are not in the box that I
> >> built
> >> > to perform the calculation
> >>
> >> Are you using AutoDock 4 or AutoDock Vina? In Vina, there is a stiff
> >> scoring function penalty for going outside the box, so the ligand is
> >> very unlikely to stray too far.
> >>
> >> Oleg
> >> --
> >> Oleg Trott, Ph.D. (Columbia University)
> >>
> >> http://olegtrott.com
> >> ________________________________________________
> >> --- ADL: AutoDock List? --- http://autodock.scripps.edu/mailing_list---
> >>
> > ________________________________________________
> > --- ADL: AutoDock List? --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
> --
> Oleg Trott, Ph.D. (Columbia University)
>
> http://olegtrott.com
>
> ________________________________________________
> --- ADL: AutoDock List? --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List? --- http://autodock.scripps.edu/mailing_list ---



      

------------------------------

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End of autodock Digest, Vol 58, Issue 22
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