Hello,
I'm trying to use CGENFF to generate CHARMM topology and parameter for a small molecule, and then convert the topology with charmm2gromacs program. I have some questions on the process.
1) How is the 1-4 parameters generated from the CGENFF file? I was not able to find the parameters corresponding to the 1-4 nonbonded parameters in the original CHARMM parameter file.
I'm trying to modify some parts of the topology and parameter obtained from PARAMCHEM(adding new atomtypes, etc) and is curious if this may result in inconsistency of generated 1-4 parameters.
2) As I understand from the CHARMM implementation paper of GROMACS, special features of CHARMM(multiple dihedrals, CMAP, etc) has been taken into the GROMACS package. I'm not sure at which step this is done. I guess maybe pdb2gmx does when it generates .top file, and this is taken into account when grompp processes .top file. Am I correct?
Thanks all in advance. I'm really appreciating the various features possible with GROMACS.
Jong Wha
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