[gmx-users] problem with pdb2gmx

Sergio E. Wong swon9 at itsa.ucsf.edu
Fri Nov 21 05:26:02 CET 2003

Dear Sirs;

  I'm new to gromacs.  I'm trying to set up a system for simulation.  The
pdb code is 2RCS.  I use pdb2gmx initially to get a topology file, I use
the -his option interactively decide the positions of the histidine
hydrogens (all have both hydrogens).  After that I used genbox to produce
a water box and I used the option -box 10 10 10.  Then I used genion to
add 8 anions.  Then I realize that I need to use pdb2gmx to produce a new
topology file that includes the anions.  So, I try to use it, but on
CYS214, the input .gro file reads CYSH (it has the thiol hydrogen),
however, I get an error message complaining about the thiol hydrogen and
it says that it can't find that hydrogen in the .rtf file for CYS2.  For
some reason, it doesn't read the file properly and thinks that the residue
type is CYS2 rather than CYSH.  I'm using the OPLS force field.  Any
suggestions would be appreciated.



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