VMD-L Mailing List

From: Paul Dennis Simonson (psimonso_at_illinois.edu)
Date: Sun Jul 06 2008 - 21:15:13 CDT

I am interested in doing a simple equilibration on my protein (3KIN).
I am trying to use the autopsf plugin, and I run into two problems:
1. I am trying to patch two segments together, but I do not know what
kind of patch to apply. Basically, the protein is dimeric, but there
are four auto-generated segments. I want to patch (twice) the end of
one segment to the beginning of the next one so that I end up with 2
protein segments. How do I do it?
2. When I ignore the patching issue and just go with the automated
output, and I choose "Solvate" and "Ionize", it seems to produce the
output files okay, but the program hangs. I am running VMD 1.86 on an
Intel Mac running OS 10.5.3. I end up having to close VMD by closing
the terminal window.

Taking my autopsf files, I then try to run a namd simulation
(basically a modified version of the water box equilibration of
ubiquitin from the tutorials), but I get the following error message:
"------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CN7

Charm++ fatal error:
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CN7

Abort trap"

I searched for CN7 in my psf file, and I find that it is associated
with ADP. What should I do so that I can get the simulation to run?

Thanks,
Paul