Hello everyone,
I am using Amber11 to do MD simulation. In order to restraint heavy atoms only I set the restraint with " restraint_wt = 10.0, restraintmask = "(:1-206 | :359-607) & !.H=" " instead of GROUP.
So where to check the restraint_wt in the output. I get only following related information in the output. So how can we can the restraint_wt or it is simply because I have not restraint the molecular at all?
5. REFERENCE ATOM COORDINATES
Mask (:1-206 | :359-607) & !.H=; matches 1865 atoms
EAMBER (non-restraint) = -122185.0850
As for the GROUP restraint, amber will give an output as follow:
----- READING GROUP 1; TITLE:
Hold the protein fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
GRP 1 RES 1 TO 200
Number of atoms in this group = 3253
----- END OF GROUP READ -----
Thanks very much with your kind help
Best wishes
Xueqin
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Received on Thu Nov 25 2010 - 07:00:04 PST
