From: Brian Radak (brian.radak.accts_at_gmail.com)
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
-- 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 e-mail: radak_at_uchicago.edu
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