[gmx-users] mktop

[Justin A. Lemkul]

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

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

and membrane protein systems:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

-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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