VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Fri May 05 2017 - 13:12:41 CDT

Hi Brian,

psf is rebuild automatically when mutator is utilized. Or did you mean it
is better to rebuild the molecule from scratch? I'd rather avoid rebuilding
the molecule because I want to save computation time for equilibration, and
because I want to have as little difference as possible with the original
system.

Thanks,

Olga

On Fri, May 5, 2017 at 9:54 AM, Radak, Brian K <bradak_at_anl.gov> wrote:

> 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
>
>
>