From: Morgan, Brittany (
Date: Thu Dec 04 2014 - 14:08:26 CST


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...

Thank you very much!


From: Josh Vermaas []
Sent: Thursday, December 04, 2014 2:12 PM
To: Morgan, Brittany;
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:


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