VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu May 04 2017 - 22:00:20 CDT

Hi Joshua,

thank you for your help. I tried mutator on my macbook and it works well,
it only fails on ubuntu. Indeed it looks as if it can't find topology
files, probably because I have an older version of vmd installed there.

Olga

On Thu, May 4, 2017 at 7:26 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Olga,
>
> Mutator ought to work. What is at the head of the error messages? In
> principle mutator for your case is super straightforward, since the only
> atomic coordinate that needs to be guessed is the proton on CE (HE2 I
> think?), but the errors you are showing indicate that the plugin didn't
> load the top_all36_prot.rtf topology file like it should have, so mutator
> is bailing out on you. If you don't feel like diagnosing the plugin, you
> can of course just do it by hand, using something like this:
>
> package require psfgen
> mol load psf old.psf pdb old.pdb ;# Alternatively, use namdbin
> old.restart.coor of a post-equilibration system
> set oldseg [atomselect top "segment P1"]
> set oldsegHSD [atomselect top "segment P1 and resid 1234"]
> $oldsegHSD set resname HSE
> $oldseg writepdb renamed.pdb
> topology top_all36_prot.rtf
> segment P1 {
> pdb renamed.pdb
> }
> coordpdb renamed.pdb P1
> regenerate angles dihedrals
> guesscoord
> writepsf p1.psf
> writepdb p1.pdb
>
> Unfortunately rebuilding the psf is just unavoidable, since the bonds,
> angles, and dihedrals change since the proton moved.
>
> -Josh
>
> On 05/04/2017 05:01 PM, Olya Kravchenko wrote:
> 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
>
>