[gmx-users] Trouble with Gromacs finding the files it needs

J. Nathan Scott scottjn at chemistry.montana.edu
Tue Nov 30 21:49:59 CET 2010

Hello Gromacs users,

I am having some difficulties with Gromacs finding the files it needs
(at least that is what I *think* is the problem) and am hoping that
someone can offer some insight. Using another user's home directory
installation of Gromacs (v 4.0.7) I was able to work my way through
Justin Lemkul's very nice lysozyme tutorial. However, now that I am
working from my own home directory installation of Gromacs (v 4.5.3) I
keep running into problems involving the addition of chloride ions in
that same tutorial (as well as in other applications). The error I'm
receiving using the newer version and installation of Gromacs occurs
when I am using grommp to prepare a file containing protein, solvent,
and ions for energy minimization:
Program grompp, VERSION 4.5.3
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype CL-
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

This is very confusing since all I am doing is using a newer
installation of Gromacs and following the exact same commands from the
tutorial. Naturally I started checking and comparing topology files
from the 2 runs to see if I could figure out what was going on. I
noticed a few differences but am unsure what to make of them.

The older version of Gromacs, for instance, has the user and host
names correct at the top of the topology file, whereas my freshly
installed version has both user and host as "onbekend", so it seems
that user and host information is not being communicated in my new
copy of Gromacs. Also, the topology file generated by the older
version has includes of the form of #include "ffoplsaa.itp", #include
"posre.itp", #include "spce.itp", and #include "ions.itp" whereas the
newer version has includes of the form #include
"oplsaa.ff/forcefield.itp", #include "posre.itp", #include
"oplsaa.ff/spce.itp", and #include "oplsaa.ff/ions.itp".

I know of course that "CL-" is the correct form of the chloride ion in
OPLSAA (I checked oplsaa.ff/ions.itp to be certain), so I am quite
baffled as to why this error is occurring. Is this indeed some sort of
path problem, perhaps? I have noted that when I use "CL" instead of
"CL-" in genion grommp has no trouble, but I believe it *should*
because I have selected the OPLSAA forcefield. I have also noted that
when I replace "oplsaa.ff/ions.itp" in my topology file with just
"ions.itp" grommp runs fine, but this worries because I don't know why
it works.

In case it makes any difference, I installed Gromacs using the
following procedure to yield MPI single and double precision versions
of mdrun and single and double precision non-MPI versions of the

./configure --enable-mpi --disable-float --prefix=/home/scott/gromacs
make mdrun && make install-mdrun
make distclean

./configure --enable-mpi --enable-float --prefix=/home/scott/gromacs
make mdrun && make install-mdrun
make distclean

./configure --disable-float --prefix=/home/scott/gromacs --program-suffix=_d
make && make install
make distclean

./configure --enable-float --prefix=/home/scott/gromacs
make && make install

Thank you very much for any help you can provide, this problem really
has me scratching my head!

J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University

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