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