VMD-L Mailing List

From: Matthew Kenney (matthew.kenney_at_cellsignal.com)
Date: Thu Aug 02 2018 - 17:19:16 CDT

Hi VMD/NAMD users,

I've been having a lot of trouble getting Alascan to work on my machine,
and I was hoping that someone could help offer some advice.

I am running to an issue where whenever I use a protein force field file
(namely top_all36_prot.rtf) and hybrid topology file (namely
top_all36_hybrid.inp), I get a whole slew of errors from psfgen that
essentially say that it cannot recognize any of the residue names in my
protein molecule (alascan uses psfgen in the backend to generate mutated
molecules in order to perform alanine scanning).

psfgen) unknown residue type SER
psfgen) unknown residue type THR
psfgen) unknown residue type LYS
psfgen) unknown residue type LYS
psfgen) unknown residue type THR
psfgen) unknown residue type GLN
psfgen) unknown residue type LEU
psfgen) unknown residue type GLN
psfgen) unknown residue type LEU
psfgen) unknown residue type GLU
psfgen) unknown residue type HSD
psfgen) unknown residue type LEU
..

I've realized that this issue is probably due to the fact that the hybrid
topology file uses single-letter codes for residue names, whereas the
protein force field uses 3 letter codes for residue names. When combined
together, the hybrid topology file cannot recognize the residues. However,
even when I change the protein force field file to match the hybrid
topology file, there still appears to be errors reading even the same 1
letter codes that the hybrid top. file is based on:

psfgen) unknown residue type S
psfgen) unknown residue type T
psfgen) unknown residue type K
psfgen) unknown residue type K
psfgen) unknown residue type T
psfgen) unknown residue type Q
psfgen) unknown residue type L
psfgen) unknown residue type Q
psfgen) unknown residue type L
psfgen) unknown residue type E
psfgen) unknown residue type H
psfgen) unknown residue type L
psfgen) unknown residue type L
..

Hoping someone might be able to provide me a solution, either by suggesting
different topology/ force field parameter files, or by suggesting some kind
of editing of the files to get this to work. Perhaps this is a silly
question, but I'm new to FEP and would really appreciate the help. Thank
you!

Best,
Matt 

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