VMD-L Mailing List

From: Radak, Brian K (bradak_at_anl.gov)
Date: Fri May 05 2017 - 08:54:51 CDT

I don't have a lot of experience with mutator, but be careful here - the structure of improper torsions is totally different for all HIS variants. The bonds need to be totally removed and rebuilt.

Personally I think the best bet is to completely rebuild the PSF after changing the resname.

But like I said, I have little idea as to what mutator actually does underneath.

Cheers,
Brian

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

________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Olya Kravchenko [ovkrav_at_gmail.com]
Sent: Thursday, May 04, 2017 10:00 PM
To: Vermaas, Joshua
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: substitute one residue without rebuilding the structure?

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<mailto: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