[Dock-fans] sphgen

Prashant Kumar prashantkbio at gmail.com
Tue Sep 1 22:01:05 PDT 2009


Dear Shivkumar,
                         Use sphgen_cpp to generate the spheres around a
receptor from your molecular surface file. You can find the source code
from  this (http://dock.compbio.ucsf.edu/Contributed_Code/index.htm) site.

On Wed, Sep 2, 2009 at 12:30 AM, <dock-fans-request at docking.org> wrote:

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> Today's Topics:
>
>   1. sphgen (Sivakumar subramaniam)
>   2. Dock and divcon (Andrei Neamtu)
>   3. atom types with chemgrid (Suhaib Shekfeh)
>   4. sphgen problem (Sivakumar subramaniam)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 1 Sep 2009 08:00:17 +0530
> From: Sivakumar subramaniam <sivabio at gmail.com>
> Subject: [Dock-fans] sphgen
> To: dock-fans at docking.org
> Message-ID:
>        <7fb49b180908311930s249fca30w6db207159aef6cd3 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Members,
>
> I am running dock 6.3, while i am running sphgen command with insph file.
> it
> does
> not formed rec.sph file as output file.  But it forms temp1.ms and
> temp3.ate
> files along
> with outsph file.  But no rec.sph file.
>
> What might be the reason for it. Kindly help me.
>
> S.Sivakumar
> Research Scholar
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> ------------------------------
>
> Message: 2
> Date: Tue, 1 Sep 2009 10:50:24 +0300
> From: Andrei Neamtu <neamtuandrei at gmail.com>
> Subject: [Dock-fans] Dock and divcon
> To: dock-fans at docking.org
> Message-ID:
>        <650c70740909010050q5d5917cakdd5c4a2171667f68 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello,
>
> I am trying to install Dock 6.3 on a Ubuntu 9.04 distro. I succeeded
> in compiling the code and I try to run now the test validation suite.
> The tests are successful up to a test where Dock is trying to find the
> divcon executable from the Amber distribution installed on the system
> (I have Amber 10)
>
> Presently, Amber 10 does not create an stand alone executable for
> divcon, but uses instead mopac6.
>
> The problem is that Dock wants to find the divcon even if I set the
> environment variable DOCK_HOME to point to the root directory of Dock
> distribution and I erase the AMBERHOME env variable.
>
> Thank you for any suggestions,
> Andrei
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 1 Sep 2009 12:00:28 +0200
> From: Suhaib Shekfeh <s.shekfeh at gmail.com>
> Subject: [Dock-fans] atom types with chemgrid
> To: dock-fans at docking.org
> Message-ID:
>        <b7ffbba40909010300o77a1197bn7a3ffde6d3fe414f at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> dear Scot and John
>
> I tried to make new file prot.table.ambcrg.ambHnew , which includes all the
> missing hydrogen types that make me problem with chemgrid
> but then I get this messaeg :
>
>  maximum number of atom types exceeded
>  increase parameter maxtyp
>
>
> how could I increase this parameter .. is it source code parameter , which
> i
> need to recombile the program after it
>
> --
> Pharmacist. Suhaib Shekfeh
> Medicinal Chemistry
> Institute of Pharmacy
> Martin-Luther-Universit?t Halle-Wittenberg
> Wolfgang-Langenbeck-Str. 4
> 06120 Halle (Saale), Germany
>
> Tel:    0049 345 55 25 043
> Fax:   0049 345 55 27 355
> Local Time : GMT + 1
> http://pc.pharmazie.uni-halle.de/medchem/mitarbeiter/shekfeh/
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> ------------------------------
>
> Message: 4
> Date: Tue, 1 Sep 2009 18:42:24 +0530
> From: Sivakumar subramaniam <sivabio at gmail.com>
> Subject: [Dock-fans] sphgen problem
> To: dock-fans at docking.org
> Message-ID:
>        <7fb49b180909010612i7d48bd05x26b57e3be314422b at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Members,
>
> I am running dock 6.3, while i am running sphgen command with insph file.
> it
> does
> not formed rec.sph file as output file.  But it forms temp1.ms and
> temp3.ate
> files along
> with outsph file.  But no rec.sph file. The OUTSPH file contain the
> following information
>
> density type = X
>  reading  rec.ms
> type   R warning exceeded # of surface points *****
>
>
> What might be the reason for it. Kindly help me.
>
> S.Sivakumar
> Research Scholar
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> End of Dock-fans Digest, Vol 64, Issue 1
> ****************************************
>



-- 
Prashant Kumar
Centre For Computational Biology and Bioinformatics
School of Information Technology
Jawaharlal Nehru University , New Delhi
Cell +91-9212136815
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