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
--
========================================
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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