[gmx-users] problem with pdb2gmx

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 21 09:00:02 CET 2003

On Fri, 2003-11-21 at 05:24, Sergio E. Wong wrote:
> 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.
You don't have to rerun pdb2gmx. Instead you have to edit the topology
manually and add 
#include "ions.itp"
somewhere, just before the [ system ] section. See chapter 5.
> Thanks
> -Sergio
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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