[gmx-users] BUG IN ffgmx.rtp for 3.2.0 beta1

John Kerrigan kerrigje at umdnj.edu
Fri Dec 19 14:05:01 CET 2003

Hi Erik-

Sorry to bother you with this.  I've noticed what appears to be a bug in
the ffgmx.rtp residue topology database for the gromacs 87 FF in your new
beta1 3.2.0 version.  This database works fine for some
polypeptides/proteins and for others I get a missing " DUM HO4 residue"
error.  I parse the starting PDB file and yet can find no HO4 residue or
DUM atom.  I tried the 43a1 force field and received no errors when
running pdb2gmx.  As a last check, I substituted the ffgmx.rtp file from
version 3.2.0 with the ffgmx.rtp file from 3.1.4 and voila, the error goes
away!  I'm thinking there might be a typo somewhere in the new version
ffgmx.rtp file.  The one difference between the two versions that I notice
is that there is a HO4 residue in the new version, which I can only assume
to be TIP4P water.  The old version does not have this residue present.



John E. Kerrigan, Ph.D.
Robert Wood Johnson Medical School
University of Medicine and Dentistry of NJ
675 Hoes Lane
Piscataway, NJ 08854

(732) 235-4473  phone
(732) 235-5252  FAX

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