AMBER Archive (2006)

Subject: Re: AMBER: leap can't assign CALA

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Sat Sep 23 2006 - 10:36:12 CDT

Thank you.

I made a mistake.
I could solve the problem by removing chainID 'B' also.
Have a nice weekend.

++++++++++++++++++++++++++++++++++++++++++++
ATOM 3002 O ALA B 391 36.570 -8.533 52.698 1.00 27.88 O
ATOM 3003 CB ALA B 391 33.800 -9.834 52.916 1.00 26.78 C
ATOM 3004 N ALA B 392 35.311 -6.882 53.557 1.00 29.62 N
ATOM 3005 CA ALA B 392 36.131 -5.822 52.978 1.00 32.31 C
ATOM 3008 CB ALA B 392 35.583 -4.461 53.392 1.00 31.59 C
ATOM 3006 C ALA B 392 37.603 -5.930 53.367 1.00 34.13 C
ATOM 3007 O ALA B 392 37.911 -6.603 54.373 1.00 35.95 O
ATOM 3009 OXT ALA B 392 38.433 -5.316 52.662 1.00 35.48 O
ATOM 3012 FE2 FE2 393 20.922 9.956 65.107 1.00 18.17 FE
ATOM 3046 O WAT 394 22.652 10.270 66.476 1.00 17.36 O
ATOM 3046 H1 WAT 394 22.583 9.472 67.052 1.00 17.36 O
ATOM 3046 H2 WAT 394 23.528 10.675 66.602 1.00 17.36 O
++++++++++++++++++++++++++++++++++++++++++++++

On 9/22/06, David A. Case <case_at_scripps.edu> wrote:
> On Fri, Sep 22, 2006, Myunggi Yi wrote:
>
> > Created a new atom named: OXT within residue: .R<ALA 392>
> ...
> > WARNING: There is a bond of 25.854368 angstroms between:
> > ------- .R<ALA 392>.A<C 9> and .R<FE2 393>.A<FE2 1>
>
> This example exposes a long-standing buglet in LEaP: The "TER " card
> separating molecules must have a space following the letters TER. This is
> probably true for official PDB files, but is just asking for trouble, since
> the missing white space is not visible in text editors, etc.
>
> For now, just edit your pdb file, and make sure that each TER card has a space
> after the "R". I'll post a patch that removes this restriction.
>
> Thanks for the report. (I hope this will solve the problem you see; if not,
> please let us know.)
>
> ...regards...dac
>
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-- 
Best wishes,

MYUNGGI YI
==================================
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Institute of Molecular Biophysics
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