[gmx-users] Group Cl not found in indexfile
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 24 20:41:39 CET 2009
SHANG Yuan wrote:
> 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:
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users