[gmx-users] problem with pdb2gmx

[David]

On Sat, 2003-11-22 at 00:47, Sergio E. Wong wrote:
> 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?
yes, depending on the force field the ions are called cl- or cl and na+
or na. 


> 
> 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
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++