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

Fri Mar 16 20:23:03 PDT 2012

Hi,

In addition to Eric's comments;
4) This post has a ligand prep script:
http://mailman.docking.org/pipermail/dock-fans/2011-December/002591.html

5) Can you find and look at sqm.out ??

6) Just as further evidence that NAD is tractable; see
dock6/parameters/leap/parm/ndp.*
(and again this is antechamber circa 2006).

scott

On Fri, Mar 16, 2012 at 02:37:54PM -0700, Eric Pettersen wrote:
> Hi Brad,
> 	Well, a few things:
> 
> 1) From your output I can tell that you are using an old version of  
> Chimera.  You should upgrade to the latest version (1.6.1) which  
> includes a more recent version of antechamber with latest bug fixes.
> 
> 2) I cannot get Chimera to fail on NAD (including old versions of  
> Chimera).  Does DockPrep work if you use it on 2h4f in regular,  
> non-"nogui" mode?  How about if you use it on 2gbp?  Also, do you even  
> want NAD present in the receptor when you attempt docking?
> 
> 3) You couldn't possibly bring up the reply log in nogui mode since it  
> creates a window.  It's irrelevant anyway since the reply log output  
> is the stuff you are already seeing on standard output (it only goes  
> into the reply log in gui mode).  For posterity, the syntax you would  
> have used to start the reply log is: --start "Reply Log".
> 
> 4) You would likely prep the ligand separately, yes.
> 
> I am taking chimera-users off the reply-to for this, since I doubt  
> most subscribers will be interested in the minutiae of this problem.
> 
> --Eric
> 
> On Mar 16, 2012, at 12:35 PM, Brad Ridder wrote:
> 
> >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?