Is it possible to rename atoms with psfgen?

From: Brian Radak (
Date: Wed Jan 28 2015 - 09:54:16 CST

I'm working on a somewhat complicated workflow utilizing psfgen and
combinations of single and dual topologies.

I can successfully apply a patch with psfgen to convert a single topology
psf into a dual topology psf. I can also "unpatch" the dual topology psf
and keep either set of the copied atoms (what you might call the "lambda 0"
and "lambda 1" sets). Obviously the lambda 0 and lambda 1 atoms have
different names. However, I'd like the resulting "unpatched" single
topology psf to always have the same standard pdb names (regardless of
which atoms I kept).

In CHARMM I would have supplemented the patch with the "RENAME ATOM"
command, but I can't readily find an analogous command in psfgen, although
pdbalias sounds very close.

Can anyone make a suggestion? I suppose, although this would be very
kludgy, that I could just use a system call to sed and change the names
that way.


Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812

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