Re: problem in generating psf file

From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Tue Nov 30 2010 - 18:44:33 CST

Hi Alex,

NAMD is choking because of the absence of an "angle" parameter in your force
field -- specifically, the (fictitious) H-H-O angle in TIP3P water. The
thing is, the CHARMM force field uses a fictitious bond between the
hydrogens in its TIP3P water model, so if you are using that you have to be
sure that you don't "regenerate angles" after building your water segment(s)
with PSFGEN. The "Solvate" VMD plugin handles this issue automatically, but
if you are manually re-building a PSF that includes water, you have to be
careful with this issue.

-Erik

On Tue, Nov 30, 2010 at 10:12 AM, Alex Liu <liu.alex77_at_yahoo.com> wrote:

> Hi,
> I have a pdb file for a system containing a channel ion. I neutralize the
> system by adding counter ions and then I generate psf file. Then load both
> psf/pdb files as in tutorial and add water box. This will generate new
> psf/pdb files for the solvated system.
> Now if I want to remove the channel ion, I have to generate new psf with
> the same number of atoms. I removed this ion form the solvated system and
> just generated the new psf file. But, after running MD, it says that:
>
> Warning: Ignored 3645 bonds with zero force constants.
> Warning: Will get H-H distance in rigid H2O from H-O-H angle.
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
>
>
> My idea is maybe I have to remove channel ion from the original pdb file,
> then generate psf again, then neutralize the system, then solvate again. if
> so, every time I want to change something in pdb file I have to re-do all
> neutralization and solvation again starting from the original pdb. Is that
> true?
> Thanks,
> Alex
>
>

-- 
C. Erik Nordgren, Ph.D.
Chemistry Department
University of Pennsylvania

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