Dear Bill
very thanks for your reply and attention.
I spent long time to solve this problem. unfortunately, since I'm beginner
in programming, I couldn't reorder coordinate of water molecules and Na+
ions.
If you are sure reordering of the coordinates will solve my problem,
please help
me about that.
ordering of atoms in gromacs trajectory file (xtc) is as follows:
1-1867 complex
1868-24085 SOL (water)
24086-24099 Na+ (ions)
On Wed, Dec 29, 2010 at 9:16 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > [different coords for amber & gromacs]
>
> Again, I wonder if you properly solved the problem of ions being
> in different places in the amber prmtop than in your gromacs
> trajectory.
>
> Bill
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 29 2010 - 23:00:04 PST
