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

Brad Ridder clustro at gmail.com
Mon Apr 9 16:41:04 PDT 2012


Hi Scott and Eric,

Okay, so I suppose the problem was not using the latest version of Chimera
when running dockprep.py. I now correctly get "dp.mol2" written to the
working directory.
Now, I am just confused to where this puts me in the 4-step process. In the
tutorial, this .mol2 file should correspond to everything up to and
including step 1g in the tutorial.
dp.mol2 has hydrogens in it, which need to be stripped away.

I have a some new questions then:

1. I need to take dp.mol2, and make rec_noH.pdb from it. Is there a quick,
easy way to do this with Chimera? e.g. open dp.mol2, strip the hydrogens,
and save the results as a .pdb file? I see this commented-out code from
ligprep.py could be useful:

#runCommand('select H')
#runCommand('delete sel')

And also this "write" command:

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/write.html#options

But how do I get python to use that "write" command? I don't understand why
there is a "write" command here, but there is a totally separate python
module "WriteMol2" just for writing .mol2 files. There is no "WritePDB."

2. I looked at the ligprep.py script, but I don't understand how to run it
yet. First, where do you specify the input file? And what format does it
have to be in? Also, there is some commented out code up top:

# $HOME/chimera/1.2470/bin/chimera --nogui ligprep.py

Is that just the command for running it from the terminal? It has no inputs
specified, so the input file appears to be "start.sdf". Am I understanding
this correctly? I am just confused because in the original message, the
person wanted to loop over many files, but as this ligprep.py script is
written, I don't see how any looping could be done since the input file is
hard-coded to be "start.sdf".

3. In the case of 2H4F, I have more than one ligand. I want to keep the
large peptide fixed (it has a long lysine pointing into the center of the
enzyme), but NAD is what I want to dock. How would I tell Chimera/Python to
choose NAD for ligand preparation?
4. The module "chimera" needs to be imported. However, I have three
versions of Chimera on my computer: 1.5.3, 1.6, and 1.6.1. How will the
Python import command know to go into the 1.6.1 directory to find the
correct, up-to-date module files? Just adding the /chimera/share folder to
the python path should work, right?
5. Is there a special procedure for deleting the other Chimera versions, or
just trash them?

All the best, and thank you so much for your help,

-Brad

On Fri, Mar 16, 2012 at 11:23 PM, Scott Brozell <sbrozell at rci.rutgers.edu>wrote:

> 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?
>



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