psfgen - pdbalias when using readpsf

From: Brian Radak (
Date: Thu Dec 15 2016 - 14:28:56 CST

I'm not sure that "pdbalias residue" is doing what is expected - can
someone enlighten me?

I am reading a pre-made psf/pdb/coor/vel set from files, but want to
change some of the topologies that are used. Specifically I want every
instance of the standard C36 residues HSD, HSE, and HSP to become HIS (a
new topology that I made and loaded an RTF for). This is essentially the
same thing as opening the PSF and PDB and running sed to replace
HSD/HSD/HSP with HIS. I thought the following would do what I want:

pdbalias residue HSD HIS
pdbalias residue HSE HIS
pdbalias residue HSP HIS
readpsf <blah>
writepsf <some new psf>
writepdb <some new pdb>

but this does not seem work as I wanted it to (the output pdb still
contains HSD residues in my test). Does pdbalias only work when using
the segment command? If so, is that a bug or a feature?


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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