AMBER Archive (2004)

Subject: Re: AMBER: Error while protonating a PDB file

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 25 2004 - 19:34:43 CST

On Thu, Mar 25, 2004, Mike wrote:
>
> I got an error while using 'protonate' on a PDB file.
>
> The error message is
>
> error in finding unit vector:
> 1 3 51.060 -11.635 48.664 51.060 -11.635 48.664
> error: case #1.100b, bond r2 has zero length.
> ip= 2 na= 3 nhyd= ***** protp(1-3,1-4)= 51.21 52.74 52.20
> 0.00-10.28-10.74-10.19 0.00 50.29 49.58 37.23 0.00

The program thinks you have two atoms in your pdb file that have the
same coordinates (51.060 -11.635 48.664). You should check to see if this
is so, of if there is any problem in atom nomenclature for the atom that
has these coordinates, or for any nearby atoms. Also, visually check
the reasonableness of the input coordinates near (51,-11,48).

...good luck...dac 

-- 

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