AMBER Archive (2009)

Subject: [AMBER] a question about umbrella sampling (US)

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Wed Feb 04 2009 - 11:12:02 CST

Dear Users,
I want to do umbrella sampling (US) for a ligand from one binding state (complex s1, used as input coordinate in input file -c) to another binding state (complex s2, used as the refence coordinate in input file -ref) with the same protein. I want to restraint RMSD of non-hydrogen atoms of the ligand in the restraint file.
 
I used the the restraint file like:
 
&rst IRESID=1, iat=532, ATNAM(1)=C1,ATNAM(1)=O5,ATNAM(1)=C6,.....ATNAM(1)=C43, r3=1.0, r4=2.0, r1=0.5, r2=1.0, rk2=30, rk3=30, &end
But I guess this is to restrain the average distance between the input coordinates to the refence coordinates for these atoms.
anyone can help me to build a RMSD restraint?
 
thanks
xiaoqing
 
 
 
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