Hi,
I'm trying to attach a carbonyl linker to Lys so that I can attach a PEG molecule to it. I have attempted so far by combining Lys , N-terminal and C-terminal topology data . But I'm having trouble deciding on the atom types I should use and the charges. Also whether I should stick to using CGENFF.
Linker and part of Lys topology file I have combined so far, ATOM CE CT2 -0.20 ATOM HE1 HA2 0.09 ATOM HE2 HA2 0.09 ATOM NE NH1 -0.70 ATOM HE HC 0.44 ATOM C C 0.51 ATOM O O -0.51
I have also attached my molecule below.
Any help would be appreciated,
Thank you
Did you try this: http://www.swissparam.ch ("This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS."
Consult the answers to this question:
https://www.researchgate.net/post/How_can_I_generate_ligand_topology_for_charmm_and_amber_force_fields_in_GROMACS
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