I am new at molecular simulations using GROMACS. So following the online tutorial for Protein-Ligand Complex by Dr. Justin, I have generated topology file for my ligand using PRODRG server for GROMOS 96 ff. As there were difference in charges in the atoms, I calculated the charges in chimera using AM1-BCC antechanmber tool. Now I want them to add into my ligand topology file for gromos. Any suggestion how should i proceed?
GROMOS parametrization relies on empirical fitting to condensed phase data. There is limited connect to QM, so your AM1-BCC charges should be viewed as a starting point in the parametrization process, and likely the correct charges will not be the same. You can certainly piece together most of the topology from existing groups, as is standard practice for GROMOS. Group transferability is a strong point in most additive force fields. See also dx.doi.org/10.1021/ci100335w
Indeed, the tutorial uses PRODRG as an example of why you should not use its output directly. People often ignore this critical detail :)
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