AMBER Archive (2009)

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

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Hello Guozhen,

This setup should work for building structures with TIP4P-Ew (2005) waters.

source leaprc.ff99SB
loadamberparams frcmod.tip4pew
m = loadpdb pdb.structure
solvateoct m TIP4PEWBOX 8
saveamberparm m top crd

Regards,
Lauren

________________________________
From: GZ Zhang <zgz215_at_gmail.com>
To: amber_at_ambermd.org
Sent: Wednesday, January 21, 2009 4:39:50 PM
Subject: [AMBER] how to use those water models off the list in amber?

Hello, All

     I want to run md simulations of water using Amber10. And I know there
are several kinds of water models in the list of solvent models.
It's of course convenient to use them. But what if I need to use some other
water models that are not in the list? Like TIP4P/2005, COS/G2,
etc. I have tried to use TIP4P/2005 model which is a modified TIP4P model,
but got topology files with parameters of TIP4P, not TIP4P/2005.

What I did is as follows:

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 not certain if the geometry
parameter(O-M distance) are also the same as that of TIP4P. Yet it's no
doubt that the TIP4P/2005 model is not correctly implemented
in the system.

I didn't find the key to this question in either amber's manual or amber's
mail archive.
Please help me, thanks.

Guozhen
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