AMBER Archive (2006)

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

From: mernst_at_tricity.wsu.edu
Date: Wed Aug 16 2006 - 13:41:02 CDT

Greetings,

I wish to run thermodynamic integration calculations for DNA containing a modified base,
using PARM99. My perturbed state for the residue of interest will contain a few atoms
that change to a different standard atom type plus others that change to dummy atoms, so
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. I could use it with DC for example, and then
edit the generated file to introduce changes rather than manually creating my frcmod
file from scratch.

Is there any tool that will allow me to generate "template" frcmod files from standard
residues as I desire? Or is there an alternate way to approach my problem? My modified
DNA is much like normal DNA, so it makes sense to alter standard parameters rather than
start with a blank slate.

Matt Ernst
Washington State University

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