I want to do simulation on a molecule thats not parametrized before. I want to use gromacs as simulation package and opls all atom forcefield. How can I parametrize this molecule to obtain dihedrals, angles and etc.
My molecule is large and webservers like prodrg and swissparam did not work for it. Can I use gaussian for obtaining parameters and build topology file by myself?
ATB and PRODRG are for GROMOS force fields; they are not applicable here.
Luckily, the OPLS literature is quite thorough in describing the parametrization methodology. OPLS, like many additive force fields, builds its molecules from model compounds. That means you likely don't have to build the entire molecule from scratch. Rather, you need to parametrize model compounds that represent any functional groups that are not already present in the force field. The QM methods are laid out well; initial parametrization is basically a recipe if you follow the literature in reasonable detail. Validation is done based on condensed phase properties, with parameters refined to match liquid phase target data.
ATB and PRODRG are for GROMOS force fields; they are not applicable here.
Luckily, the OPLS literature is quite thorough in describing the parametrization methodology. OPLS, like many additive force fields, builds its molecules from model compounds. That means you likely don't have to build the entire molecule from scratch. Rather, you need to parametrize model compounds that represent any functional groups that are not already present in the force field. The QM methods are laid out well; initial parametrization is basically a recipe if you follow the literature in reasonable detail. Validation is done based on condensed phase properties, with parameters refined to match liquid phase target data.
you can use ANTECHAMBER (AMBER tools) to generate the parameter and topology file. Then, you can use script amb2gmx.pl (Originally written by Eric Sorin, Pande lab, Stanford. Modified by David Mobley and John Chodera, Dill lab, UCSF.) to convert AMBER .prmtop and coordinate files to gromacs topology and coordinate files.
check this tutorial http://ambermd.org/tutorials/basic/tutorial4b/
Assign atom types using OPLS-AA and start a simulation to see how many parameter you are missing. Some times a good estimate based on analogy of the functional groups is much better than parametrizing a new molecule.
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