Dear Case
Happy Christmas
> Now you can edit the com.mdcrd file, find the coordinates of the
troublesome
water, and see if there is a problem or not.
I found coordinates of a certain water molecule (residue 3501) in certain
time from .mdcrd file (amber trajectory ):
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 O WAT X3501 10.100 43.710 29.100 0.00 0.00
ATOM 2 H1 WAT X3501 60.630 51.900 31.190 0.00 0.00
ATOM 3 H2 WAT X3501 61.280 52.590 31.090 0.00 0.00
END
also
I found coordinates of the same water molecule (residue 3501)in the same
time from .xtc file (gromacs trajectory):
CRYST1 62.664 62.664 62.664 90.00 90.00 90.00 P 1 1
ATOM 1 OW WAT X3501 54.910 60.930 16.030 0.00 0.00
ATOM 2 HW1 WAT X3501 54.420 61.290 15.290 0.00 0.00
ATOM 3 HW2 WAT X3501 55.530 60.320 15.630 0.00 0.00
END
these two coordinate are not same.while for another residue except water
molecule (for example: one residue of protein)
two coordinates obtained from amber and gromacs are the same, exactly.
How to fix this problem?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Wed Dec 29 2010 - 03:00:04 PST
