From: Morgan, Brittany (
Date: Thu Dec 04 2014 - 12:00:21 CST


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