On Wed, Dec 29, 2010, leila karami wrote:
>
> 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.
OK...You have localized the problem, and it occurs before Amber is involved.
I've never used this conversion script, so can't help out there. Maybe
someone on the list has an idea. Otherwise, you may have to approach the
gromacs people (or whoever put together the program you are using.)
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 29 2010 - 06:00:04 PST
