AMBER Archive (2007)

Subject: AMBER: AMBER 9 - visualization of MD trajectory by MOE

From: dinko.x.ziher_at_gsk.com
Date: Wed Nov 07 2007 - 06:45:41 CST

Hi all,

We would like to visualize MD trajectories (MD simulation in periodic box)
generated by AMBER9 with MOE by creating appropriate SVL script.

Our problem at the moment is that when reading the coordinates from mdcrd
file the periodic box seems to be tilted by 45 degrees in one direction
and the origin seems to be shifted. To correct the coordinates we would
need information about the tilt angle and the translation offset used, but
we cannot find it in the prmtop file.
Could you tell us which conversion is used in the mdcrd file for
coordinate conversion?

Regards,

Dinko Ziher

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