Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules

From: leila karami <>
Date: Thu, 30 Dec 2010 10:13:25 +0330

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+

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 <> 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

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
AMBER mailing list
Received on Wed Dec 29 2010 - 23:00:04 PST
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