[gmx-users] problem with pdb2gmx

[Sergio E. Wong]

Thanks :).  So, I included the #include "ions.itp" line in the top file
manually, and lowered the number of water molecules (some of the waters
were replaced by ions).  I also included under [system] the ions.  But
when I try to run grompp, I get either:

1.  I get an error because it doesn't recognize Cl as a molecule type (I
think it should, but it isn't recognizing it)

2. I remove the Cl ions from the [system] section and I get an error
because the number of atoms in the *.top and *.gro files are different.

Is there a way around this?

Thanks

On Thu, 21 Nov 2003, David van der Spoel wrote:

> 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.
> ________________________________________________________________________
> 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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