Dear all,
I want to do a molecular dynamic simulation using Charmm27 force field in gromacs. I generate the ligand topology by http://www.swissparam.ch server. It takes .mol2 file as a input and provides .crd & .psf & .par & .itp file format.
Then i use pdb2gmx command for generating protein topology. It gives .itp and .gro file.
I add ligand.itp file in protein.itp but which file i add in .gro file for creating the complex.
Please suggest me. I also read the http://www.swissparam.ch/SwissParam_gromacs_tutorial.html. But i did not found any significant answer.
"6. Merge the protein and ligand coordinates. Insert the ATOM lines from the ligand.pdb into the conf.pdb file, right after the line for the ion CAL. Atoms will be automatically renumbered in the next step."
Note that the tutorial does not use .gro format, it uses .pdb format instead. Either is acceptable in GROMACS, which supports many different coordinate file formats.
Dear Justin sir,
I am new in molecular dynamic simulation.
I want to ask about charmm27 force field. Please suggest me any tutorial link if available.
When we choose gromacs force field and generates the topology from prodrg server. then we add the ligand.gro file in to protein.gro and increase the atom number.
But here i generate the topology from http://www.swissparam.ch/ server. it not provides ligand. gro then which file i add protein.gro for making complex.
Please suggest me sir. I read many tutorial in internet but i did not found any relevant answer.
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