AMBER Archive (2009)
Subject: Re: [AMBER] a question about umbrella sampling (US)
From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 04 2009 - 11:20:46 CST
you're right that the restraint you used isn't what you want. I'd
suggest reading the targeted MD section of the manual (page 99 for
amber10) and then asking more specific questions about what still
isn't clear. also take a look at the sample files for this in the test
cases in test/tgtmd.
On Wed, Feb 4, 2009 at 12:12 PM, xiaoqin huang <xqhuang1018_at_msn.com> wrote:
> 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?
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