Re: [AMBER-Developers] A Parameter File Editor (that DOESN'T pipe everything through leap);

From: Jason Swails <>
Date: Thu, 6 Oct 2011 20:20:29 -0400

On Sun, Oct 2, 2011 at 1:18 PM, case <> wrote:

> On Fri, Sep 30, 2011, Jason Swails wrote:
> > The program I wrote,, should be easy to use (hopefully) because
> it
> > operates just like ptraj and cpptraj (only instead of playing with
> > trajectories it plays with topology files).
> Sounds great! Can you ask it to strip certain residues, then output the
> corresponding prmtop? Of can ptraj/cpptraj now do this? [I need a "real"
> prmtop, not just for visualization.]

An update: now it can. rdparm was able to strip water (or maybe any general
solvent?), but NOT arbitrary atoms (it could delete bonds, angles, or
dihedrals, though). As you alluded to at the end, though, is that rdparm
doesn't actually create a working prmtop that could be used for anything
besides visualization (and indeed prints out a pre-Amber7 prmtop version
that doesn't even have FLAG and FORMAT lines). I'll let Dan comment fully
about cpptraj, but as far as I knew it was capable of producing
visualization-capable topologies for stripped solvent, but not one that
worked for calculations.

The functionality in parmed is fairly general. You can delete any "mask"s
that you want and output a calculation-ready topology file. If any atom is
involved in bonds/angles/dihedrals, those parameters are removed (it's
documented in the current AmberTools.lyx file in the master repo). For
performance sake (to make the process take ~1 second to strip solvent as
opposed to an indeterminate amount of time), I recalculate all of the
pointers for all of the parameters, so the topology files will look very
different, even though for the couple systems I tested it for the energies
worked out exactly as expected through a short minimization. parmed cannot
currently delete bonds, angles, or dihedrals, although that functionality
wouldn't be too hard to add if people thought it could actually be useful
(and it would properly update the excluded atoms list as well).

I'd appreciate anybody that wants to run the code through the wringer a
little and point out any issues they may be having (especially with the mask

All the best,

(As a side note, it will help people build systems with X waters by creating
a topology file that gets close to that number, then removing the extras via
this strip command or automate the creation of MMPBSA-ready topologies)

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Oct 06 2011 - 17:30:04 PDT
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