[AMBER] a question about umbrella sampling (US)

From: xiaoqin huang <xqhuang1018.msn.com>
Date: Wed, 4 Feb 2009 12:12:02 -0500

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
 
 
 
_________________________________________________________________
Windows Live™: E-mail. Chat. Share. Get more ways to connect.
http://windowslive.com/howitworks?ocid=TXT_TAGLM_WL_t2_allup_howitworks_022009_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 06 2009 - 01:10:55 PST
Custom Search