AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Feb 06 2009 - 16:35:55 CST

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 group 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

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