From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sun Mar 30 2008 - 14:50:29 CDT

Hi VMD and NAMD community,

I am using NAMDEnergy, which is working nicely for some of my solvated
protein systems. However, I need to analyze bunch of dcd trajectories
generated much earlier with NAMD2.5 by another user. These systems had a
bond specified twice in the psf file. So, when I try to use NAMDEnergy for
these trajectories, I get:
~~~~~~~
Running:
/software/NAMD/namd2 namd-temp.namd

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Duplicate bond from atom 1949 to atom 1950

Charm++ fatal error:
FATAL ERROR: Duplicate bond from atom 1949 to atom 1950
~~~~~~~~

Can you suggest a way to tell NAMDEnergy to override the two-time bond
specification in the psf file?
(Even if it considers the particular bond twice, it won't matter, as it is a
very big system, and I am looking at non-bonded interactions between protein
and solvent).

Thanking you,
Neelanjana Sengupta

-- 
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Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
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