AMBER Archive (2009)

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

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Wed Feb 04 2009 - 16:23:12 CST

thanks, but
1) I met a strange error.
    I calcualte the coordinate-averaged distance between the input coordinate and the reference coordinate for the group of atoms as defined in the restraint file in my last email. it is 0.678 A.
but from the DUMPAVE output file, such distance is 73.808 A.
 
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&wt type='DUMPFREQ',istep1=1 &end &wt type='END' &end DISANG=dus1.f DUMPAVE=w11.out
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2) I donot know how the restraint file is read in and how the distance is calculated during the MD.
 
 
3) yes, I have done tgtmd, and I want to calculate the PMF along the RMSD changes, or the distance change as reaction coordinate.
 
 
xiaoqing
> Date: Wed, 4 Feb 2009 12:20:46 -0500> Subject: Re: [AMBER] a question about umbrella sampling (US)> From: carlos.simmerling_at_gmail.com> To: amber_at_ambermd.org> > 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, r
4=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_at_ambermd.org> > http://lists.ambermd.org/mailman/listinfo/amber> >> > _______________________________________________> AMBER mailing list> AMBER_at_ambermd.org> http://lists.ambermd.org/mailman/listinfo/amber
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