Re: Is it possible to rename atoms with psfgen?

From: Jim Phillips (
Date: Thu Jan 29 2015 - 13:11:46 CST


Atom renaming isn't supported in psfgen, but I think you can do your
entire "unpatching" process more cleanly in the latest VMD, which can now
write psf files containing full bond/angle/dihedral/improper/... data from
an atom selection. In VMD you can rename atoms something something like:

   [atomselect top "resname FOO and name BARX BARY"] set name BAR

Then to write out:

   set a [atomselect top "...lambda 0 atoms..."]
   $a writepsf a_lam0.psf
   $a writepdb a_lam0.pdb

If you want to do this to the output trajectory then use catdcd.


On Wed, 28 Jan 2015, Brian Radak wrote:

> 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.
> Thanks,
> Brian
> --
> 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:

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