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

From: leila karami <karami.leila1.gmail.com>
Date: Thu, 30 Dec 2010 14:04:03 +0330

Dear Bill

my gromacs trajectory file (xtc) contains 2500 frames.

I converted 2 frames of that to pdb file and then I reordered coordinate of
Na+ ions with water molecules in a editor.
then I obtained amber trajectory file (mdcrd). 1) when I open .prmtop and
new .mdcrd file by VMD, problem of length
of the water molecules was solved.
2) I found coordinates of a certain water molecule in those 2 frames in
gromacs and amber trajectory files,
coordinates are the same.
thus, as you said, reordering of coordinate of Na+ ions with water molecules
solved my problem. but I did
reordering just for 2 frames and manually.

how to do this reordering for all of the frames in gromacs trajectory file
(xtc) or in the converted pdb file?

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Thu Dec 30 2010 - 03:00:05 PST
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