AMBER Archive (2006)

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

From: David Mobley (dmobley_at_gmail.com)
Date: Wed Aug 16 2006 - 16:51:47 CDT

Matt,

> 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.

I was never able to figure out how to do this, although let me know if
you have any success. I think what I ended up doing for something
similar was to write a script to parse the parameter files and grab
all of the force field parameters I might need. I actually ended up
doing this on the GROMACS side (since I'm running simulations in
GROMACS), but in principle it probably could be done on either end.

David
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