Hi Jason
Thanks for the help. It should work. Let me try this program.
Piotr
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, April 25, 2011 11:52 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] printing out the actual set of force field
parameters assigned to a molecule
Indeed! I just wrote such a thing recently. What it actually does is print
out an frcmod file from a topology file... is that what you're looking for?
Check out the program ante-MMPBSA.py installed as part of AmberTools 1.5.
If you just run the program "ante-MMPBSA.py -p <input_prmtop>", it will
create three files: _AnteMMPBSA_.off, _AnteMMPBSA_.frcmod, and
_AnteMMPBSA_.leaprc. The first one is the Amber OFF library that contains
every residue in the system, the second is a complete frcmod file that
prints every parameter found in the prmtop, and the last is the leaprc that
loads everything properly in Leap. I originally wrote it as a way of
preparing MMPBSA prmtops, since the force field for each part of the system
has to be the same, and extracting the parameters from the complex topology
file is the easiest way of assuring that if people didn't create all of the
topology files in the beginning (as they should).
I think I gave Francois a version of the frcmod creator some time ago, but
it didn't have the OFF file creator. rdparm also does something similar,
but it doesn't dump it in a leap-readable frcmod file like ante-MMPBSA.py
does.
As a final disclaimer, though, I think there's something I haven't gotten
quite right with the OFF file, since only sleap will read them successfully
IIRC; tleap just segfaults (but sleap does create *correct* topologies with
it).
HTH,
Jason
On Mon, Apr 25, 2011 at 11:36 AM, Piotr Cieplak <pcieplak.burnham.org>wrote:
>
> Dear All
> Is there any practical way available for printing out the actual list
> of parameters assigned by Leap to the molecular system, which are in a
> readable format and are reported in the actual units as they are in the
> parmXX.dat files?
> I mean - the printout of the information in the format/units that
> was long time ago produced by the PARM program.
>
> Piotr
>
>
>
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> AMBER-Developers.ambermd.org
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 25 2011 - 12:30:06 PDT
