VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Dec 04 2014 - 12:45:12 CST

On Thu, Dec 4, 2014 at 1:00 PM, Morgan, Brittany
<Brittany.Morgan_at_umassmed.edu> wrote:
> Hello,
>
>
>
> I have a very large system (protein, peptide, lipids, water) that I need to
> perform a mutation on. Since the Mutator plugin is capable of dealing with
> solvated systems, I used that. The mutation was performed correctly but the
> PSF has 2 extra angle terms that I need to delete before I run the
> simulation in NAMD.
>
>
>
> Through searching the mailing list, I found the Topotools plugin and I've
> been trying to use it to delete the extraneous angles from the psf. I am
> using VMD version 1.9.1 with topotools 1.2.

please update to the latest VMD beta version. topotools is at version 1.5 now.
you can also try to only update topotools with the package from here:

https://sites.google.com/site/akohlmey/software/topotools

but i would recommend to update VMD and benefit from the many
improvements to the rest of VMD as well.

> Here is one way I have tried:
>
>
>
> mol new mypsf.psf waitfor all
>
> package require topotools
>
> topo numangles
>
> (returns 150973, which agrees with the original psf)
>
> topo delangle A B C

what is that command supposed to do? the documentation clearly states
that those three terms have to be atom indices.

>
> mol reanalyze top
>
> topo numangles
>
> (still returns 150973)
>
>
>
> Other ways include deleting a bond and using "topo retypebonds" and "mol
> reanalyze top", but the number of bonds doesn't change. I've tried writing
> out using both "writepsf" and "animate write psf" and there is no change to
> the psf. I've tried loading the PDB, and not loading the PDB. Topotools does
> not return anything (0, 1, or error messages) when I use delbond or
> delangle.
>
> The reason the Mutator plugin gives me extra angles is that the
> crystallographic water has an extra bond in the input PSF. I thought if I
> could remove that and re-run Mutator, this problem wouldn't occur, but I
> can't delete a bond from the PSF, either.
>
>
> Any suggestions will be greatly appreciated,

before you spend much more time on working with a huge system, why
don't you create a small minimal test system and check out, if you
have the same kind of problem. if yes, you can post the files and
scripts here and we can have a closer look.

axel.

>
>
>
> Brittany Morgan
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.