AMBER Archive (2009)

Subject: Re: [AMBER] how to use those water models off the list in amber?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Jan 22 2009 - 07:29:41 CST

On Wed, Jan 21, 2009, GZ Zhang wrote:
>
>
> tleap -f leaprc.ff99SB
> loadamberparams frcmod.tip4p05 (modified O-M site distance)
> loadoff tip4p05.lib (modified charge distribution file, using gleap utility)
> mol=loadpdb TIP_216.pdb (standard 216-water box, retrieved from amber
> examples)
> set mol box 18.0 (pbc)
> saveamberparm mol z.top z.crd
>
> I checked the resulting topology file and found that the charge distribution
> is the same as that of TIP4P model.

It's hard to tell without more information. Does the off file use "WAT"
as the residue name? It's very odd that Amber would pick up the original
TIP4P charges, since the default water is TIP3P. So, I could see that you
might get TIP3P charges if the default was leaking through, but I don't
see (offhand) any easy way for the TIP4P charges to be getting into your
prmtop file. Use the standard debugging stuff: try variations of things
to try to track where the charges are coming from.

As already noted, if by TIP4P-2005 you mean the Horn, Swope, Pitera,
Head-Gordon TIP4P-EW, then that model is already built in.

...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber