[gmx-users] Group Cl not found in indexfile

SHANG Yuan spl at ust.hk
Tue Nov 24 20:09:23 CET 2009

  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........
   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.
   would any kind spirit help?
   Thanks in advance.


More information about the gromacs.org_gmx-users mailing list