VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu May 04 2017 - 16:58:38 CDT

Hi all,

this must be something simple, but I couldn't come up with a good solution.
I need to change only one histidine residue from HSD to HSE and run my ABF
simulation to compare the outcome. The structure is already well
equilibrated, so I am wondering if there is a way to do this substitution
without rebuilding this system from scratch (to avoid long equilibration of
the whole molecule)? Can I do substitution through atom selection somehow
and just switch one HSD for HSE?

I tried using mutator plugin, but it gives me errors of this sort:

...
...
psfgen) unknown residue type THR
psfgen) unknown residue type LEU
psfgen) unknown residue type GLY
psfgen) extracted 172 residues from pdb file
psfgen) Info: generating structure...psfgen) unknown residue type THR
failed!

Can mutator plugin be used for my goal and what am I doing wrong?

I will appreciate your input!

Thanks,

Olga