VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Mar 30 2008 - 15:02:58 CDT

How about deleting the bond from the psf? Or regenerating a proper psf
for the same system with the same number of atoms?
Jim et al., any comments on how the duplicate bond would have behaved in
namd2.5? Would it just have been treated as a single bond or would there
have been two bonds present in the dynamics?

Best,
Peter

Neelanjana Sengupta wrote:
> 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
> --
> ****************************************
> Neelanjana Sengupta, PhD student
> Dept. of Chemistry
> Univ. of California-Irvine
> Irvine, CA 92697
> ****************************************