AMBER Archive (2009)

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

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Dr. Case and Lauren,

     Thanks for your comments.
     The TIP4P/2005 (Abascal, Vega, JCP, 123, 234505) is not the same as
TIP4P/Ew.
The former is aimed at a general purpose, while the latter is optimized for
biological
systems. They are both modifications of the original TIP4P model.
(http://en.wikipedia.org/wiki/Water_model)<http://en.wikipedia.org/wiki/Water_model>

     I indeed used "WAT" in the off file. Changing into other keyword(like
TP4) caused error
when loading the pdb file.

     Thanks.
     Guozhen

On Thu, Jan 22, 2009 at 8:29 AM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> 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
>
>
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• Previous message: Shan-ho Tsai: "[AMBER] REM_hybrid test fails on AIX"
• In reply to: David A. Case: "Re: [AMBER] how to use those water models off the list in amber?"
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