[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
somewhere, just before the [ system ] section. See chapter 5.
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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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