On Sun, Sep 22, 2024, Husak Michal via AMBER wrote:
>I see water atoms are recognized by atomtypes in Antechamber (gaff and gaff2)
>as:
>ho-oh-ho
>Insted of correct
>hw-ow-hw
The notion of "correct" atom types is tricky: atom types are only internal
to Amber, and Junmei Wang chose oh/ho. There is nothing wrong with that
choice. It is probably better to use an more standard model for water. All
of Amber's "standard" water models use OW/HW. (Note that atom types are
case-sensitive, so OW/HW is not the same as ow/hw; if there is a problem
with ow/hw definitions in gaff2.dat, then the simplest thing is not to use
those atom types.)
....good luck...dac
p.s. cc-ing to Junemi, he case he wants to look at ow/hw entries in
gaff2.dat.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 24 2024 - 12:00:02 PDT
