AMBER Archive (2009)

Subject: [AMBER] distance calculation by reading in the restraint file

From: xiaoqin huang (
Date: Fri Feb 06 2009 - 11:52:56 CST

Hi, all
anyone can tell me what is wrong here.
I used the DISANG=dus1.f in the input file to read in the restraint file dus1.f
and the content of the dus1.f is:
 &rst IRESID=1, iat(1)=197,ATNAM(1)=CB,ATNAM(1)=OG, iat(2)=532, ATNAM(2)=O31,ATNAM(2)=C32,ATNAM(2)=O33,ATNAM(2)=C34,ATNAM(2)=C35,ATNAM(2)=C37,ATNAM(2)=C39,ATNAM(2)=C41,ATNAM(2)=C43, r1=0.00,r2=4.650,r3=4.650,r4=20.00,rk2=80,rk3=80, &end------------------------------------------
it is supposed to restrain the distance between the group1 atoms and the group 2 atoms, and according to the amber8 manual, such distance is calcuated as the DISTANCE BETWEEN THE AVERAGEED COORDINATES FOR GROUP 1 ATOMS AND THE AVERAGED COORDINATES OF GROUP 2 ATOM.
 Here are comments from the DISANG input file: Number of restraints read = 1
                  Done reading weight changes/NMR restraints--------------------------------------------------------
and the fist number of the dumped file is 4.450.
THEN, I calculated the distance according to the definition in the manual, i.e. coordinates-averaged, using the input coordinates, it is 3.927.
it is so different, where is the error?
and how to get more reaing-in information about the restratints from the MD output file?
it is better to output a piece of information like " matches ??? atoms" in the output file.

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