VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sun Mar 30 2008 - 15:51:45 CDT

Hi,
Is there a straightforward way to 'delete' a bond and rewrite a system? I
believe I cannot justopen up edit the psf file (or can I?). I would rather
take that path if possible, because these systems (partially degenerated
proteins) were not generated by me, and I don't really want to tinker with
the system setup.

Thanks,
Neelanjana

On Sun, Mar 30, 2008 at 1:02 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>
wrote:

> 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
> > ****************************************
> 

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