I have to calculate the electrostatic potential and I would to include NAD+
into the calculation. I am normally using the server PDB2PQR but it cannot
convert the NAD+ molecule - is there an easy way to get out of this problem?
Any help or advise appreciate. Thanks in advance.
Per Jr. Greisen wrote:
> I have to calculate the electrostatic potential and I would to include
> NAD+ into the calculation. I am normally using the server PDB2PQR but it
> cannot convert the NAD+ molecule - is there an easy way to get out of
> this problem?
NAD+ is composed of Nicotinamide, ribose and ADP. You could take partial
charges of the Ribose and ADP subgroups from the CHARMM nucleic acids
force field (top_all27_na.inp).
For Nicotinamide you might be able to construct charges using the PARSE
parameter set (J. Phys. Chem. 1994,98, 1978-1988), though I am not
familiar with it. You might get more reliable results from a single
point QM calculation for pyridine and Mulliken population analysis.
Alternatively, you could prepare crude nicotinamide partial charges by
simply spreading the +1 Nitrogen-charge over the pyridine ring according
to its locations in the resonance electronic structures. Partial charges
for carboxamide functional groups can also be found in the CHARMM22
protein force field.