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

[Justin A. Lemkul]

J. Nathan Scott wrote:
> 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.
> 

The directory structure has changed as of version 4.5, and ion names have been 
standardized across the force fields.  The proper [moleculetype] of the chloride 
ion (in oplsaa.ff/ions.itp) is indeed "CL" while the *residue name* is "CL-" and 
the atom name (which is what you pass to genion) is "CL."

So, if you have added a line like

CL-   8

in the [molecules] directive of your topology (like in my tutorial), then you 
get the fatal error.  The [moleculetype] name is what you enter here, not the 
residue name.

I haven't updated my tutorial for version 4.5.x, but perhaps I should.  If you 
follow what I say exactly, you will have problems in the newer version.

-Justin

> 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
> tools:
> 
> ./configure --enable-mpi --disable-float --prefix=/home/scott/gromacs
> --program-suffix=_mpi_d
> make mdrun && make install-mdrun
> make distclean
> 
> ./configure --enable-mpi --enable-float --prefix=/home/scott/gromacs
> --program-suffix=_mpi
> 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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================