I found the error is because the reading in the restratint file in MD when reainding the following file:
----------------------------------------------------
&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
--------------------------------------------------------
I tested, when only 1 atom of each group, the distacne is correct.
when two atoms of each group, only the last ATNAM(1) and ATNAM(2) are read in , and the dumped distance is the distance between the last atom of each group
when I changed to ATNAM(1)=CB,OG, andATNAM(2)=O31,C32, only the fist atom of each group is read in and the distance is dumped out.
I used amber8, and then tested amber9, the error is the same.
I looked the bug list of amber8 and amber9, but can not find a fix for this error.
anyone can help me?
xiaoqing
> From: xqhuang1018.msn.com> To: amber.ambermd.org> Date: Fri, 6 Feb 2009 12:52:56 -0500> Subject: [AMBER] distance calculation by reading in the restraint file> > > 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.> > SO, IN THE MD OUTPUT FILE, I see:> > -------------------------------------------------> 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.> > > thanks> > xiaoqing> > > > > > > > > > > > > > > > _________________________________________________________________> Windows Live™: Keep your life in sync. > http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t1_allup_explore_022009_______________________________________________> AMBER mailing list> AMBER.ambermd.org> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Feb 08 2009 - 01:12:06 PST
