[gmx-users] problem with grompp and atomtype

Anna Marabotti anna.marabotti at isa.cnr.it
Thu May 10 13:04:10 CEST 2007

Hi all,

I'm trying to simulate the MD of a protein with a ligand. Since it is the
first time, I followed exactly (at least, I think so!) suggestions from
"GROMACS tutorial for drug-enzyme complex" by J. Kerrigan. I started from
the PDB coordinates of the complex, I extracted the coordinates of the
ligand and created a .itp file for the ligand using the PRODRG server. Then
I submitted the protein alone to pdb2gmx, and then I manually edited the
.pdb and the .top files in order to re-introduce the coordinates of the
ligand into the protein. Therefore, I opened the .pdb file of the protein
created by pdb2gmx, and pasted the coordinates of the ligand obtained by
PRODRG (changing the n. of residue to continue numbering), and I edited the
.top file by adding #include "lig.itp" in the ff statement, LIG in the [
molecules ] section etc. Then I created the box with editconf, solvated it
with genbox and started grompp before neutralizing the -5 charge of the
protein with genion.
The grompp output gave me a fatal error:

Source code file: toputil.c, line 61

I don't understand why and where grompp is searching for atom type CH3. I
already checked the user list but did not find any suggestion. Could anyone
help me?
I'm attaching here files obtained from PRODRG program.

Many thanks in advance and best regards
Anna Marabotti, Ph.D.
Laboratorio di Bioinformatica e Biologia Computazionale
Istituto di Scienze dell'Alimentazione, CNR
Via Roma 52 A/C
83100 Avellino (Italy)
Tel: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: amarabotti at isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna.htm
"If you think you are too small to make a difference, try sleeping with a
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