[gmx-users] NADP in ffG43a1.rtp
burisch at bph.rub.de
Tue Dec 20 15:18:11 CET 2005
David van der Spoel wrote:
> Don't think so. The entry has only two phosphates, and it is the lower
> group in the picture that is missing. After a look in a biochemistry
> book it seems that this is in fact NAD+, rather than NADP+.
yes, and it's called NAD+ in the GROMOS manual (the residue code is
NADP like in GROMACS though...).
Satyan, what you are looking for IMHO seems to be NDPH, NDPP or NDPHN
(note the charge differences between NDPH and NDPP in the pyridine
ring). The single 2'-phosphate is unfortunately protonated at least
once (NDPH), like always in GROMOS...
I posted a partial topology for an unprotonated terminal phosphate a
couple months ago, perhaps it may help.
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