AMBER Archive (2009)

Subject: RE: [AMBER] distance calculation by reading in the restraint file

From: xiaoqin huang (
Date: Fri Feb 06 2009 - 17:28:59 CST

thanks a lot, now I am on the right way.
> Date: Fri, 6 Feb 2009 17:35:55 -0500> From:> To:> Subject: Re: [AMBER] distance calculation by reading in the restraint file> > On Fri, Feb 06, 2009, xiaoqin huang wrote:> > > > 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 gro
up is read in and the distance is dumped out.> > > > It's not clear what your desired constraint is here. In the above, you> give several values for ATNAM(1), for example. Namelist readers will> always take just the last value. > > Look carefully at the instructions for igr1(). If you want groups of> atoms, you need to use GRNAM1, etc. not ATNAM. But I recommend that you> first construct a restraint just using atom numbers, not names. Make sure> it does exactly what you want. Then you can try to change it to atom> names. Work with simple things first.> > I know it's not always simple, and Amber10 has what we hope is a more> intuitive interface.> > ...dac> > _______________________________________________> AMBER mailing list>>
Windows Live™: Keep your life in sync.
AMBER mailing list