AMBER Archive (2003)

Subject: Re: AMBER: Restraints

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 06 2003 - 17:26:47 CST

On Thu, Nov 06, 2003, Steve Seibold wrote:
>
> Restrain oxygen atom of Ligand
> 100
> FIND
> * OH * *
> SEARCH
> RES 554 554
> END
>
>
> Here is the the OUTPUT file:
>
> GROUP 2 HAS HARMONIC CONSTRAINTS 100.00000
> ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW
> GRAPH NAME = * SYMBOL = OH TREE SYMBOL = * RESIDUE TYPE = *
> GRP 2 RES 554 TO 554
> Number of atoms in this group = 0
>
>
> P.S. I have made sure that "OH" is the atom type in both Leap and in my pdb
> files for this ligand.

You may be misinterpreting what the word "symbol" means. Atom types would
never be in a pdb file. Why don't you try to give the atom name instead
of the symbol, and see if that helps?

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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