[gmx-users] mktop

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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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