Dear Members:
I have some questions concerning group coordinate averaging:
the predefined upper distance bounds are 2.8 (as in the example below),and the group averaged result is r3= 5.71, is this enlargement of upper distance restraint mainly due to 1/r(-6) group averaging as indicated in igr1 and igr2?
I also read in the amber manual that IR6 is responsible for average position calculation(If IR6 = 0, center-of-mass averaging will be used. If IR6=1, the r−6 −1/6 average of all interaction distances to atoms of the group will be used.), Where do I change the IR6 value?
And is there is a possibility of turning off group averaging and use upper distance bounds as predefined by user.
# 0 AMB 20-2:93 0 AMB 20-1:93 2.80 (# 93:20 Double Ambig) &rst ixpk= 93, nxpk= 20, iat= -1, -1, r1= 1.30, r2= 1.80, r3= 5.71, r4= 6.21, igr1=2203,1059, 449,1593, 113,1257, igr2=2205,2206,1061,1062, 451, 452,1595,1596, 159, 160, 1303,1304, &end
# 2 ARG HG+ 3 ARG HD+ 4.50 (# 61:20 Unique 2.58, 5.48 A) &rst ixpk= 61, nxpk= 20, iat= -1, -1, r1= 1.30, r2= 1.80, r3= 5.67, r4= 6.17, igr1= 28, 29, igr2= 55, 56, &end
Thank you very much
Yours sincerely
----------Fei TanBeijing NMR CenterPeking UniversityCollege of Life Science100871
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jun 12 2016 - 22:00:02 PDT
