[Chimera-users] [Dock-fans] Help with antechamber

Brad Ridder clustro at gmail.com
Fri Mar 16 12:35:55 PDT 2012 

Hi Eric,

I tried the dockprep.py file you pointed to me a few emails ago. It seems
like its exactly what I am looking for. The only problem is I get an error
at the moment; I also have two other questions about it.

ep.py file you pointed to me a few emails ago. It seems like its exactly
what I am looking for. The only problem is I get an error at the moment; I
also have two other questions about it.

Here is the command I used:

./chimera --nogui pdb:2h4f $DESKTOP/dockprep.py

The program then returns a bunch of text on what its doing. When adding the
charges to the ligands with the AM1-BCC method is when the error pops up.
Here is the (slightly abridged) error message, plus a few lines back:

*Running ANTECHAMBER for residue NAD
Running ANTECHAMBER command:
/home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/antechamber
-ek qm_theory='AM1', grms_tol=0.02, tight_p_conv=0, scfconv=1.d-10, -i
/tmp/tmplP08co/ante.in.mol2 -fi mol2 -o /tmp/tmplP08co/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2

(NAD) Total number of electrons: 344; net charge: -1

(NAD) Running:
/home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/sqm
-O -i sqm.in -o sqm.out

(NAD) Error: cannot run
"/home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/sqm
-O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

(NAD) Running:
/home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(NAD) Running:
/home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Error while processing /home/abhay/Desktop/dockprep.py:
Failure running ANTECHAMBER for residue NAD
Check reply log for details*

I am not sure what the problem is. $AMBERHOME and $DOCK_HOME are not
defined, but that only seemed to cause problems before. Perhaps they need
to be defined now?
I would give you the reply log, but I don't know how to find it. I tried
using:

$ ./chimera --start Reply_Log --nogui pdb:2h4f $DESKTOP/dockprep.py

I also tried reply_log, Reply_log, reply_Log, ReplyLog, replyLog, Replylog,
and transposing --start and --nogui. None of those worked either. The
program immediately returns:

*Starting extension 'Reply_Log' failed* (or whatever the pertinent
permutation of "reply_log" happens to be.)

Assuming this can be fixed easily, I have one more question: this appears
to only prepare the receptor for docking. What about prepping the ligand?
Does that need its own new script?

Thank you so much for your help,

-Brad

On Wed, Feb 29, 2012 at 7:08 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> This previous posting to the dock-fans list seems to be more directly
> pertinent:
>
> http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
> On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote:
>
>  Hi Brad,
>
> I am cc'ing this to the chimera list.
>
> I think that you should write a python script to run DOCK prep on the
> command line.  See the following:
>
> http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html
>
> For other example scripts see the following:
>
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html
>
> You should not have to specify the AMBERHOME path.  This is done
> internally to chimera.
>
> as an aside, It is unnecessary to run antichamber with sudo.
>
> I hope this helps,
>
>  Trent E. Balius
> Graduate Student, Rizzo Group,
> Department of Applied Mathematics and Statistics,
> Stony Brook University.
> Office: Math Tower 3-129, Phone: (631) 632-8519
> URL: http://www.ams.sunysb.edu/~tbalius/
>
>
>  -----Original Message-----
> From: Brad Ridder <clustro at gmail.com>
> To: dock-fans <dock-fans at docking.org>
> Sent: Wed, Feb 29, 2012 4:38 pm
> Subject: [Dock-fans] Help with antechamber
>
>  Hi Dockfans,
>
> My name is Brad; I am a grad student in the dept. of chemical engineering
> at Purdue University.
>
> We are experimenting with DOCK for various drug discovery work. At the
> moment, I am trying to do execute all of the "dock prep" commands through
> the Terminal, since it is not practical to do large volumes of Dock Prep by
> hand through the CHIMERA GUI.
>
> Corresponding to what is in the DOCK tutorial, I am on "Receptor and
> Ligand Preparation." I got reduce to work, in order to add hydrogens.
>
> Now, I am trying to get antechamber to work, in order to add the charges,
> but it is not working. Here is the command I am running:
>
> *sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o
> $DESKTOP/3GLRcharged.mol2 -fo mol2*
>
> Which returns the error:
> *
> Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use
> "mopac.sh" in the work directory
>
> Cannot open CONNECT.TPL , exit
> The atom number exceeds the MAXATOM, reallocate memory*
>
> I looked around in the dock6 directory, and found a folder called
> "parameters/antechamber", which contains CONNECT.TPL. I figured this is
> what should be the $AMBERHOME directory.
> For DOCK_HOME, I figured it should be the dock6 folder.
>
> Here is what I have in my .bash_profile file in my home folder.
>
> *export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber'
> export DOCK_HOME='/home/.../DOCK6.5/dock6'*
>
> I also tried using the "amber11" folder that comes with CHIMERA as
> AMBERHOME, but to no effect.
>
> I don't actually have AMBER installed on my computer, but since CHIMERA
> can add charges without actually requiring the purchase of AMBER, I do not
> think that is the problem.
>
> I did not know what to do with "mopac.sh." I ran the script, but it says
> it needs input files.
>
> What am I doing wrong that is preventing antechamber from executing
> correctly?
>
> --
> Bradley James Ridder
> Chakrabarti Group
> Graduate Student
> School of Chemical Engineering
> Purdue University
>
>
>  _______________________________________________
> Dock-fans mailing listDock-fans at docking.orghttp://mailman.docking.org/mailman/listinfo/dock-fans
>
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>
>
>
>


-- 
Bradley James Ridder
Chakrabarti Group
Graduate Student
School of Chemical Engineering
Purdue University
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