Anna Marabotti a écrit :
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
FATAL ERROR: ATOMTYPE 'CH3' NOT FOUND
There is nothing wrong in you procedure. For the moment, proDRG outputs
atom types for the deprecated gromacs force field (ffgmx). You need to
alter these atom types in order to get the proper ones (i.e. the ones
coming from the force field you're using).
In a first *rough* approach, you can compare the atom types presents in
share/gromacs/top/ffgmx.atp (the one you have from proDRG)
to
share/gromacs/top/ffG45a3.atp (for the force filed G45a3 for instance)
Please pay great attention to atom types since changing the atom does
not provide a straight-forward conversion from the old FF to the new one.
Atom types are not everything, you'll need to check bonds, angles,
dihedrals, and overall, if your ligand is correctly described with these
modifications on the itp file.
I'll add a section on the wiki when it's up to be more explicit (kinda
sort of updating the tutorial).
Note there is a proDRG beta 2.5 mentionning gromacs 96.1 but for now i
have no idea about the forcefield used, its validation state, and my
question to Dr. van Aalten about this beta server version has not been
answered yet (if someone on the list has an explanation, i'm opened to
explanations).
Cheers,
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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