On Tue, Oct 12, 2010, oscarjiao.gmail.com wrote:
>
> I've been playing with Antechamber and tleap lately. Got this error when I
> was trying to solvate a single water molecule in a box of TIP3P waters.
> Error: A residue defined as a "fast 3-point water" is not defined by a
> triangle of three bonds. Residue 1 contains 2 bonds.
>
> The prmtop file shows the ATOM_TYPE of the alien water as oh ho ho, as
> opposed to OW HW HW for the TIP3P water. What is the default model for a
> water molecule in AMBER? Can I just force the water (solute) into a TIP3P
> water.
Don't use gaff for water, just solvate one WAT residue (TIP3P by default):
>
> source leaprc.ff99SB
> solvateBox WAT TIP3PBOX 9
> saveamberparm WAT prmtop inpcrd
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 13 2010 - 07:30:04 PDT
