VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Dec 04 2014 - 14:53:13 CST

On Thu, Dec 4, 2014 at 3:08 PM, Morgan, Brittany
<Brittany.Morgan_at_umassmed.edu> wrote:
> Josh,
>
>
>
> You are absolutely right: I was using the 1-based indices from the psf file,
> not zero-based indices. Everything works perfectly now. If Topotools
> included a message saying "that bond/angle/whatever does not exist", I
> probably would have realized what the problem was without having to pester
> the mailing list...

this is a deliberate choice.

topotools is designed to be a middleware and all input checking is
supposed to be done on the upper level code. furthermore, because of a
design decision that topotools considers the intersection of an
atomselection and inputs, topotools cannot know whether a mismatch
happens in error or deliberately. ...and more importantly, adding such
kind of checks would needlessly convolute the code and likely have a
massive performance impact.

if you access lower-level APIs from the C library or other toolkits,
similar issues can happen.

axel.

>
>
>
> Thank you very much!
>
> Brittany
>
> ________________________________
> From: Josh Vermaas [vermaas2_at_illinois.edu]
> Sent: Thursday, December 04, 2014 2:12 PM
> To: Morgan, Brittany; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Topotools not changing psf
>
> Hi Brittany,
>
> One word of caution: topotools 1.2 didn't handle cross terms (needed for
> CMAP) correctly. If you have a protein system using CHARMM27 or 36, those
> CMAP terms will be blown away if you regenerate the psf with topotools. The
> beta version of VMD comes with a new version of topotools that fixes this
> problem (and many others).
>
> Now back to your issue: In principle, so long as A B and C are replaced with
> the appropriate atomic indices (zero based VMD indices, not 1-based like you
> have in the psf file itself), this totally should have worked. Something you
> can try if you are happy with the bondlist is to let topotools guess angles
> from connectivity:
>
> topo setanglelist [list ]
> topo guessangles
>
> However it also sounds like you are having issues deleting bonds using
> topotools, so I suspect you may have gotten tripped up by using the wrong
> index. If a "deleted" bond or angle is not present, there is currently no
> message telling the user this, it will instead just silently do nothing. The
> methods also do not return any value even when they delete the bond or
> angle, so no news is not indicative of success or failure. :(
>
> Could you give a few more details? Maybe a snippet of the psf that contains
> the three atoms you are trying to de-angle and what you used for A B and C?
>
> -Josh Vermaas
>
> On 12/04/2014 12:00 PM, Morgan, Brittany 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.
>
>
>
> 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
>
> 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,
>
>
>
> 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.