[gmx-users] problem with pdb2gmx
David
spoel at xray.bmc.uu.se
Sat Nov 22 09:29:00 CET 2003
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
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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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--
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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