-------- Original Message --------
Subject: Water model => amber port to gromacs ? => OR
Date: Mon, 10 Nov 2008 01:22:07 -0800
From: Chih-Ying Lin <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
CC: gmx-users@gromacs.org
HI
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
Lin
-------------------------
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.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
