ram bio wrote:
Dear Justin,
Thanks for the information.
Initially, i just wanted to run a simulation of protein-ligand in water
solvent . I renamed the topology.top generated from mktop to ligand.itp;
and included the ligand.itp line in the topol.top file generated from
the pdb2gmx. During the pdb2gmx command, i used opls FF. The
coordinates of ligand used as input for mktop were added to the output
of pdb2gmx (process.pdb - only protein coordinates), so that the
structure file along with ligand coordinates (processlig.pdb) can be
used for further steps. I doubt whether the procedure followed by me is
correct, as when i execute grompp command to add ions i am getting errors :
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
ERROR 1 [file ligand.itp, line 291]:
No default Ryckaert-Bell. types
..........
-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526
Fatal error:
[ file ligand.itp, line 397 ]:
Atom index (0) in dihedrals out of bounds (1-53).
This probably means that you have inserted topology section "dihedrals"
in a part belonging to a different molecule than you intended to.
In that case move the "dihedrals" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
The commands executed to reach the grompp step are as follows:
pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
editconf -f processlig.pdb -o procent.pdb -princ
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
I have attached the topol.top, ligand.itp and procentsolv.gro files for
your information, Please let me know your suggestions to fix this error.
The ligand.itp file is trash. Most of your atoms have zero charge (except for a
few that have +/- 1...yikes!) and on line 397 (as cited in the error message)
atom 0 is referenced, which of course does not exist, since numbering starts
with 1. You also have some exotic atom types present, and thus bonded
parameters cannot be assigned, as grompp complained earlier.
You need a better quality topology, and perhaps a different force field that
might be suited for doing these simulations.
-Justin
Thanks,
Pramod
On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
ram bio wrote:
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid
bilayer. I have generated the topologies for the ligand using
MKtop. The output from the MKTOP gives the top file, but not the
coordinate/structure file. Please let me know if any tutorial is
available for merging the output of mktop into gromacs MD
simulation.
You can #include any molecule topology in a system .top, provided
you have the right format:
http://www.gromacs.org/__Documentation/File_Formats/.__itp_File
<http://www.gromacs.org/Documentation/File_Formats/.itp_File>
There is no tutorial for using mktop with a protein-ligand/membrane
system, but there are tutorials for protein-ligand complexes:
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
and membrane protein systems:
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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