AMBER Archive (2004)

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

From: David A. Case (case_at_scripps.edu)
Date: Sat Mar 27 2004 - 16:46:43 CST

On Thu, Mar 25, 2004, Madan wrote:
>
> I have checked the pdb file and i din't see any duplicate entry of the
> coordinates.
>
> I have given the part of the PDB file which has the coordinates of
> interest.(I have separated it by giving space for convenience to locate).
>
> I would greatly appreciate if you could tell is there any problem in the
> atom nomenclature for the atom that
> has these coordinates.
> ATOM 331 N LYS 57 52.764 -9.209 47.546 1.00 13.54
> ATOM 332 CA LYS 57 51.728 -9.191 48.547 1.00 13.24
> ATOM 333 C LYS 57 51.862 -7.988 49.442 1.00 19.58
> ATOM 334 O LYS 57 50.873 -7.515 50.000 1.00 21.28
> ATOM 335 CB LYS 57 51.728 -10.468 49.370 1.00 38.70
>
> ATOM 336 CG LYS 57 51.060 -11.635 48.664 1.00 38.79
>
> ATOM 337 N GLU 58 53.083 -7.500 49.611 1.00 18.00

The file is missing the coordinates of all the rest of the heavy atom side
chain atoms for Lys 57, beyond the CG atom. For this reason, protanate
is unable to calculate the postions of hydrogens beyond CG either.

Assuming that my analysis is correct, this is a bug in the sense that the
program should recongize such inputs and give a better error message.

The immediate workaround is probably not to use protonate for these
coordinates. Are you sure this step is required? (The plastocyanin tutorial
is probably over-zealous here; it is not always required to run protonate,
since LEaP can add protons as well...)

....dave case 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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