[gmx-users] Group Cl not found in indexfile

[Justin A. Lemkul]

SHANG Yuan wrote:
> Hi,gmx-users,
>   I'm following Kerrigan's "GROMACS Tutorial for Drug-Enzyme Complex", but
> encounter with some problems（my GMX version is 4.0）.
>   firstly, after "genion -s trp_b4ion.tpr -o trp_b4em.gro -nname Cl -nn 9"
> command, I add "Cl 9" at the end of "trp.top" file, and the following
> "grompp" command will always fail,complaining "No such moleculetype
> Cl",for "GROMOS96",only "CL- 9" work here.After correct this error, I go
> on through this tutorial and come with a second problem........

Ion nomenclature is force field-specific.  The tutorial you refer to is using 
ffgmx, not Gromos96.  You can refer to ions.itp for the nomenclature for each 
given force field.

>    Just after energy minimization, I type "grompp -f em.mdp -c
> trp_b4ion.gro -p trp.top -o trp_b4ion.tpr", the program
> indicates:"Group Cl not found in indexfile". I change the "Cl" in the
> line "tc_grps=protein sol IN4 Cl" of "pr.mdp" file to "CL" or "CL-",but
> neither can fix this problem.

This step refers to preparing a .tpr file for input into genion, thus prior to 
the addition of ions (b4ion = "before ions") and hence why they are not found. 
It looks like you're repeating a previous step.

Also note that the use of those tc-grps is inappropriate.  Ions and small 
molecules should never be coupled separately.  It may work fine for the 
tutorial, but in actual simulations will usually lead to a crash.  See here:

http://www.gromacs.org/Documentation/Terminology/Thermostats

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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