Hi,
I wish to simulate a ligand-protein system..I have used
the prodrg server to create the .itp file for my ligand. I
have done gaussian charge calculation for my ligand using
the chelpg method. how should i incorporate the gaussian
charges into my .itp file. should i copy the charges for
heavyatoms and polar/aromatic hydrogens only or i have to
compensate for the charges calculated for the non polar/non
aromatic hydrogen atoms. waiting for your reply. Thanks so
much
Short answer: You should do whatever is recommended for parameterizing
things for the force field you're using.
Pessimistic answer: It may be a bad idea to compute charges for an
all-atom case using QM and then try to convert these to a united atom
force field.
David
Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA
Cell - 662 380 0146
Office - 662 915 1286
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