Nagy, Peter I.
PNAGY at UTNet.UToledo.Edu
Wed Aug 13 00:26:01 CEST 2003
Dear Gromacs Users!
I have a CYS residue with a palmitoyl group on that, replacing the thiol hydrogen. When I downloaded the hydrated membrane bilayer model, GROMACS understood the DPP code of the.pdb file as DPPC. This molecule contains both
regular and phophate-ester groups, but it was an independent unit. What will
GROMACS do with a thiol ester on CYS, and how would the program handle the aliphatic chain?
I assume that I will have to modify some parameter files and adding MD parameters for the C-S-C(=O)-C-C subunit. Please give me some clues where and how to start.
Thanks, Peter Nagy
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