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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 30 2010 - 03:00:05 PST
