VMD-L Mailing List
From: Brian Radak (bradak_at_anl.gov)
Date: Thu Dec 15 2016 - 14:48:01 CST
So is there no way to do this internally? There's no general way to
rebuild a PSF on-the-fly without knowing all of the segments beforehand
and having them in separate PDBs - right?
I guess I can always add a "renameresidue" command (although boy is that
ugly) similar to the "renameatom" command. Probably better would be to
create a "rename" command that can be used variously as "rename atom" or
"rename residue". And here I thought I was done futzing up psfgen after
2.12 was released!
On 12/15/2016 02:40 PM, Peter Freddolino wrote:
>> On Dec 15, 2016, at 3:28 PM, Brian Radak <bradak_at_anl.gov> wrote:
>> 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?
> Yes it does only work when using segment commands, and this is a feature. pdbalias only applies to entries being read from topology files. The set of commands that you have never use topology files, they just read and then re-write existing information from a psf. Using sed or totally rebuilding the psf with that aliasing in place would probably be a cleaner way to accomplish what you’re trying to do here.
> Quoting the psfgen manual (http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf):
> pdbalias residue
> Provide translations from residues found in PDB files to proper residue names read in from
> topology definition files. Proper names from topology files will be used in generated PSF and PDB
>> Brian Radak
>> Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>> 9700 South Cass Avenue, Bldg. 240
>> Argonne, IL 60439-4854
>> (630) 252-8643
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov