AMBER Archive (2002)

Subject: Re: change topology

From: Bill Ross (photoriot_at_yahoo.com)
Date: Thu Mar 28 2002 - 03:45:49 CST

> I have to select some rezidues from my topology
> file and to create a new topology with selected
> residues only. I think RDPARM should be useful but
> my colleagues discouragded me. Does anybody know
> a way how to do this?

In Carnal you could define a GROUP and, using the
prmtop/inpcrd, write that group to pdb, then in leap
use loadpdb and saveamberparm.
 
A complication would be that if a chain is broken,
you'd need to put a TER card at the break, and
possibly
use loadpdbusingseq to force the residues at the
breaks
to not use terminal types.

Bill Ross

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