[gmx-users] Water models for amber03

[Justin A. Lemkul]

Jack Shultz wrote:
> Hi all,
> 
> I think I'm having a problem with the water models. Clearly ther are
> differences in these tip3p models. I can rename the ffamber_tip3p
> files to overwrite existing tip3p files. I don't want to do that
> because I want the option of choosing the amber ones at run-time.
> pdb2gmx does not accept a request for
> -water ffamber_tip3p or -water amber_tip3p
> 

The only way I have found to use the ffamber_tip3p is to manually modify the 
topol.top after pdb2gmx (i.e., vi or sed), since the Amber force fields are not 
standard within Gromacs.  I suppose you could somehow modify the pdb2gmx code to 
accept different options, but it's probably a lot easier to replace the text in 
the post-pdb2gmx topology yourself.

-Justin

> Are these the only options I can use?
> -water 	 enum 	 spc 	 Water model to use: with GROMOS we recommend
> SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c
> 
> $ ls -l *tip3* *spc*
> -rwx------+ 1 jshultz None   1377 Mar 17 11:22 Copy of tip3p.itp
> -rwx------+ 1 jshultz None 106028 Feb 27 18:46 ffamber_tip3p.gro
> -rwx------+ 1 jshultz None    638 Feb 27 18:46 ffamber_tip3p.itp
> -rwx------+ 1 jshultz None    638 Feb 27 18:46 ffamber_tip3p_heavy.itp
> -rwx------+ 1 jshultz None     36 Mar 17 11:21 flexspc.itp
> -rwx------+ 1 jshultz None     37 Mar 17 11:22 flexspce.itp
> -rwx------+ 1 jshultz None   1402 Mar 17 11:22 spc.itp
> -rwx------+ 1 jshultz None  29266 Mar 24 07:40 spc216.gro
> -rwx------+ 1 jshultz None   1142 Mar 17 11:22 spce.itp
> -rwx------+ 1 jshultz None 106028 Feb 27 18:46 tip3p.gro
> -rwx------+ 1 jshultz None   1377 Mar 24 07:40 tip3p.itp
> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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