Protein-Ligand Complex new ligand Parameters input into .str INQUIRY?

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1

Hello Gromacs Forum:

I have generated new parameters for a ligand due to penalties, accordingly before executing the below command beneath the Generate the JZ4 Topology with CGenFF heading:

python cgenff_charmm2gmx.py JZ4 jz4_fix.mol2 jz4.str charmm36-jul2022.ff

I believe that via default the proper procedure is to firstly change the the penalized parameter values to the re-parameterized values correct?

For example I would change the original charge value of 0.483 below from within the originally generated .str file:

ATOM C7 CG2RC0 0.483 ! 34.554 6 C 3 4 6 1 5 1

to the reparamterized -0.906 below from within the ffTK generated .1psf file:

10 X 3032 14C C7 CG2RC0 -0.906 12.0107 0

Your affirmation would be great, thanks if you know:)

2

Hi @mjsubach,

I would follow the same approach by first updating the .str file with the reparameterized values and then running cgenff_charmm2gmx.py. To verify the results, you could compare single-point energies on the same ligand configuration in GROMACS (using the output from cgenff_charmm2gmx.py) with those from CHARMM or NAMD (using the modified .str file).

Best,
Marius

3

Hello Marius thank you for your kind update/affirmation:).