AMBER Archive (2002)

Subject: Re: Can I use belly and ntr at the same time?

From: David A. Case (case_at_scripps.edu)
Date: Wed Oct 16 2002 - 10:45:49 CDT

On Wed, Oct 16, 2002, sxzheng wrote:

> How can I use belly and ntr at the same time? And how to restrain the
> backbone of the protein.

(I have to answer quickly, before dap says "use interface: :-))

>
> My input file like:
> nmropt=1,
> .....
> ibelly=1,ntr=1,
> &end
> &wt
> type='TEMP0',istep1=0,istep2=200,
> value1=100,value2=300.0,
> &end
> &......
> &end
> Restrain heavy atoms
> 5.0
> FIND
> * CT * *
> * CA * *
> * CB * *
> * OS * *
> SEARCH
> RES 1 529

You need (two) END cards here to finish the group specification for the ntr
section. Then the belly group specification begins. They are *not* part of
the same group.

> ----belly =residues 15a
> RES 1 1
> RES 61 171
> END
> END
>
> the out file gives:
> RESTRAINTS:
> No valid redirection requests found
> ** No restraint defined **
> Done reading weight changes/NMR restraints

You left out much of your input file...did you expect to have NMR restraints?

The best thing to do is to include a line

DISANG=dummy

right after the "&wt type='END' &end" line. Then make a zero-length file
called dummy, if you have no restraints. (This won't be necessary in the
next release).

In summary, the mdin file should look like:

  title
 &cntrl
   nmropt=1, ibelly=1, ntr=1, ...
 &end
 &wt .... &end
 &wt type='END', &end
DISANG=dummy
  title for ntr input
 5.0
RES 1 52
END
END
  title for belly input
RES 1 1
END
END

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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