Hi
I am getting strange results when I analyze my trajectory files in Carnal. I
get a rms of 20-30 angstroms for my monomer protein. I know this is
incorrect because when I superimpose (using another program) my initial
structure with my MD (after 200ps)strucure there is only about a 1.2
angstrom rms. My input for carnal looks as follows:
FILES_IN
PARM p1 1EBV_watox.prmtop;
STREAM s1 PGHS2_21.mdcrd;
FILES_OUT
TABLE tab1 PGHS2_21rms;
DECLARE
GROUP gALL (RES 1-552);
RMS r1 FIT gALL s1;
OUTPUT
TABLE tab1 r1;
END
It (rms) rises from 0 ? 25 Angstroms in 200 ps. The PGHS2_21.mdcrd is for
200ps MD simulation.
MANY THANKS for any help.
Steve
Received on Sat Mar 08 2003 - 20:53:01 PST
