Fwd: [gmx-users] mktop

[ram bio]

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  files for your information,
Please let me know your suggestions to fix this error.

Thanks,
Pramod





On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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