[gmx-users] [Fwd: Water model => amber port to gromacs ? => OR]

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 10 12:58:30 CET 2008

-------- Original Message --------
Subject: Water model => amber port to gromacs ? => OR
Date: Mon, 10 Nov 2008 01:22:07 -0800
From: Chih-Ying Lin <chihying2008 at gmail.com>
To: mark.abraham at anu.edu.au
CC: gmx-users at gromacs.org

The thing is the definition of atom type, OW and H in gromos 96 are
different from tip3p.itp, OWT3, HW.

same thing as other tip*p.itp.

How to fix this?

Thank you


Please keep GROMACS correspondence on the mailing list.

The atom type name doesn't matter for purposes of having a topology file 
that matches a coordinate file. Only the molecule ordering, atom 
ordering and atom names matter. Thus from a technical point of view, you 
could substitute any 3-centered water model that had the same atom names 
and ordering merely by substituting in and out the name of an .itp file, 
or using a #define. If you inspect tip3p.itp you will see that some of 
this chicanery is going on.

It's conceivable the atom names differ for different water models. If 
you want to keep the same coordinates, then you'd best rename the atoms 
in the structure file. If you don't mind building different coordinates, 
then you can strip the waters away and re-invoke genbox.


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