[gmx-users] genbox

John Kerrigan kerrigje at UMDNJ.EDU
Mon Nov 25 14:25:10 CET 2002


I have encountered this problem with the Windows port of Gromacs (3.1.2).
I get a blank topology file.  The easiest solution is to just leave out
the -p *.top in the genbox command line (genbox does not need the topology
file other than to edit it for you).  Edit the topology file yourself.
Add the line for the number of solvent molecule (obtain from genbox output
or your new gro file) at the end of your top file.  In addition, you may
need to add the #if "FLEX_SPC" statement (look at sample topologies from
demo, etc.).

Hope this helps.


John E. Kerrigan, Ph.D.

Dept. of Pharmacology
University of Medicine and Dentistry of New Jersey
Robert Wood Johnson Medical School
675 Hoes Lane
Piscataway, NJ 08854

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

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