Re: [AMBER] Help with solvating organic molecule with input .prmtop file

From: Jason Swails <>
Date: Thu, 1 Mar 2012 15:33:32 -0500

On Thu, Mar 1, 2012 at 12:28 PM, Andy Ballard <>wrote:

> >
> >
> > A possible alternative to "top2ff" is -- is that program
> > in your $AMBERHOME/bin? I can't remember if it was released with
> > AmberTools 1.5 or not. If so, will dump a force field
> > file with _every_ parameter in your prmtop file (including all of your
> > parameters), something I don't think top2ff does. will
> also
> > dump a full frcmod and full OFF file with every parameter and residue in
> > your system if you want to use that. You can then load this back into
> > tleap (after sourcing any other force fields) to override any previous
> > force field definitions.
> >
> > If it's not present, you'll have to use top2ff, although there will be
> more
> > options in the upcoming AmberTools release.
> >
> I've tried using top2ff, and it gets most things right, but not all.
> It sounds like is the program I need, but unfortunately
> its not in my $AMBERHOME/bin directory. Is there somewhere I could
> download it, or does it have dependencies etc. that my current amber
> version wouldn't support?

Looking back, it was not included with AmberTools 1.5, but it was an
incredibly simple script (the main code that does the work is present in
AmberTools 1.5). That script was really just a wrapper around a single
function call: amberParm.frcmod() function in the AmberParm python class.
 You can use that class directly in a python interpreter if you are
familiar with Python at all (or if you just follow the instructions below).
 So something like this:

swails.Computer /scratch/swails $ $AMBERHOME/bin/python
>>> from chemistry.amber.readparm import amberParm
>>> l = amberParm('adfda.capped.parm7')
>>> l.frcmod('my_frcmodfile.frcmod')
Warning: AmberParm.Frcmod() does not work for 10-12 non-bonded prmtops yet!
Amber force field modification (my_frcmodfile.frcmod) finished!
>>> quit()
swails.Computer /scratch/swails $ ls -lth | head -n 2
total 96K
-rw-r--r-- 1 swails swails 7.4K 2012-03-01 15:25 my_frcmodfile.frcmod

This will only work if you installed Python with AmberTools 1.5. If you
didn't, you'll need to set PYTHONPATH=$AMBERHOME/bin and then launch your
default python to get that behavior. There's a program being released with
AmberTools 12 that is a more complete wrapper around this class and offers
the extractFrcmod function as an option when modifying topology files.


> Thanks,
> Andy
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Mar 01 2012 - 13:00:02 PST
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