AMBER Archive (2006)

Subject: Re: AMBER: NAD ??

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 08 2006 - 08:49:31 CST

On Wed, Nov 08, 2006, Urszula Uciechowska wrote:
>
>
> Unknown residue: DP number: 314 type: Terminal/last

This should be your clue: LEaP thinks you have a residue named "DP" which it
doesn't know anything about. Checking the pdb file:

ATOM 2298 CG LEU 319 27.999 128.267 54.811 1.00 0.00 C
ATOM 2299 CD1 LEU 319 27.226 128.530 53.525 1.00 0.00 C
ATOM 2300 CD2 LEU 319 28.149 129.529 55.656 1.00 0.00 C
TER
ATOM 2310 P1 NDP 320 29.167 148.439 45.205 1.00 0.00 P1+
ATOM 2311 O1 NDP 320 29.899 148.499 46.507 1.00 0.00 O1-
ATOM 2312 O2 NDP 320 29.176 149.723 44.453 1.00 0.00 O1-

Note that everything after the TER card is in the wrong column. Information in
pdb files is column-specific, so you will have to fix this before you can
proceed.

...good luck...dac

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