AMBER Archive (2006)

Subject: Re: AMBER: generate "template" frcmod from standard residues?

From: David Mobley (dmobley_at_gmail.com)
Date: Fri Aug 18 2006 - 11:13:08 CDT

Matt,

I think you are pretty much stuck with parsing the relevant force
field file. The frcmod file is usually a way of filling in guesses for
parameters which are NOT present in the relevant force field file.
These are usually generated by prmchk or by hand. Basically, the force
field files are pretty similar to frcmod files except they contain the
actual parameters, not just guesses. So that's where you want to look.

Assuming you know what gaff/amber atom types you are interested in,
this isn't really that hard.

David

On 8/17/06, mernst_at_tricity.wsu.edu <mernst_at_tricity.wsu.edu> wrote:
> >> I need a frcmod file. But from the manual and mailing list it seems that
> >> only parmchk generates frcmod files automatically, and it only generates
> >> entries for missing parameters or types. I would like to generate a frcmod
> >> file that contains all entries for a residue, not just the missing ones.
> >
> > This is just a guess: have you tried creating a almost-empty gaff.dat file?
> > That is, one that has just one bond, one angle, etc which are not in your
> > system. It seems to me that then parmchk would not find any of the needed
> > parameters, and would provide a template that included all of them.
> >
> > ...dac
> If I do that, won't the template be devoid of assigned parameters? I want the parameters
> to initially reflect the standard force field parameters for a standard nucleotide so
> that I can alter them a bit rather than parameterizing the entire residue by hand. Maybe
> altered amino acids and nucleotides are less commonly used than I imagined.
>
> Matt Ernst
> Washington State University
>
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