VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Mar 30 2008 - 16:02:30 CDT

You can just edit the psf in a text editor; just change the number of
bonds, delete the excess bond, and be careful to maintain the formatting
of the bond lines (this will require carefully re-wrapping some text if
the offending bond is not at the end). You can see a description of the
psf format in the appendices of the namd tutorial.
Best,
Peter

Neelanjana Sengupta wrote:
> 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 <mailto: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
> > ****************************************
>
>
>
>
> --