I have a molecule decane 1-thiol. I have to create its .itp file because I have to include it into .top file. Can someone please give me tips on how to do that?
PRODRG2 - will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated.
This depends on which force field you want to use. If you want to use GROMOS force field, you may try ATB (http://compbio.biosci.uq.edu.au/atb/index.py) server for initial force field paramters of the molecule.
PRODRG2 - will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated.
But if you use these parameterization servers, please check the outcomes carefully! Sometimes, they don't get the charges or even atom types correctly. See the Gromacs homepage for information about the "parameterization of novel molecules" and have a look at this very nice publication. http://pubs.acs.org/doi/abs/10.1021/ci100335w
Copy and paste the coordinates from pdb file of the molecule to the PRODRG server. It will generate the gro and itp files. Then you can include that itp file into the .top file.
ATB and PRODRG servers are good options to generate itp and gro files of the molecule as suggested above. If you are planning to use Charmm ff then u can try Swissparam server. Be carefull with PRODRG generated files. It usually gives wrong energies so always keep a check on these and correct accordingly.
I want to run the Docked-complex simulation using OPLS forcefield for which I have used mktop to generate topology file of ligand for OPLS forcefield. Now, I have the ligand topology.top file but how to use this for simulation process ? How should I include the ligand information to the opls processed .gro file of protein ? Can I get the ligand.gro file for opls forcefieldby any mean?
i generate topolgy from PRODRG for ethylene carbonate. but this topology file didnt work for md simulations. it shows error like '[molecule type]' in the .top file. please anyone help me in this regard. thank you