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

[John Kerrigan]

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.

Regards,

John

-----------------------------------------
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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