On 12/20/2012 09:13 AM, pcl wrote:
Well what works for me is I convert cgenff and merge it with charmm36 (you only
have to do this once per cgenff version), then I have paramchem generate cgenff
charges for the ligand. Then I convert the output of paramchem (charges) to
.rtp format. I also have to create .hdb entries. Paramchem may also generate
additional cgenff atom interactions (dihedrals or impropers) that may not exist
by default, I usually convert and add those to forcefield's .itp files. Then
pdb2gmx will work on the ligand pdb.
but isn't there is a script to do so in Gromacs webiste, which can
convert the output from parachem into Gromacs .itp format? although I
didn't try it hard, because I don't find any documentation to use it
correctly.....
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