VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Apr 01 2008 - 10:55:05 CDT

Hi Neelanjana,
if you look at your new psf carefully, you'll note that the column
spacing is not preserved near the end of the bonds section. Each index
field should occupy a total of 8 characters (including spaces), but 9
are occupied in your file near the end of the section. Fixing this
should fix your problem.
Peter

Neelanjana Sengupta wrote:
> Hi Peter,
>
> I followed your instruction, so that my new psf file has exactly the
> same format, with only the double specification of the bond removed.
> It was actually 2 bonds specified twice (between 1949-1950 and 1949-1951).
>
> However, when I load up the modif.psf, I get:
>
> Info) Using plugin psf for structure file modif.psf
> ERROR) Error reading bond information.
> Info) Analyzing structure ...
> Info) Atoms: 28004
> Info) Bonds: 0
> Info) Residues: 28004
> Info) Waters: 0
> Info) Segments: 4
> Info) Fragments: 28004 Protein: 0 Nucleic: 0
> 0
>
> At this point, I am clueless. I am attaching both the original
> (old.psf) and the modified (modif.psf) files. I would be VERY grateful
> if you could point out to me where the problem lies.
> Thanks,
> Neelanjana
>
>
> On Sun, Mar 30, 2008 at 2:02 PM, Peter Freddolino
> <petefred_at_ks.uiuc.edu <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> 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>
> <mailto: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
> > > ****************************************
> >
> >
> >
> >
> > --
>
>
>
>
> --