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

[J. Nathan Scott]

On Tue, Nov 30, 2010 at 2:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>

Ahhh, now it all makes sense! Thanks very much for your helpful answer Justin!

By the way, should I be concerned about "onbekend" in the user and
server names? I don't particularly care what is in those fields, but
am slightly worried that they indicate I have something configured
incorrectly, which could then affect the functionality of the
software.

-Nathan

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