AMBER Archive (2009)

Subject: Re: [AMBER] tleap maximum coordination exceeded

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Nov 17 2009 - 22:45:55 CST

On Tue, Nov 17, 2009, Jack Shultz wrote:

>
> These are the GLU 1 atoms before using babel to add H
> [boincadm_at_vps test2]$ grep "GLU 1" receptor.pdb
> ATOM 1 N GLU 1 -20.050 8.920 -4.700 1.00 0.00
> ATOM 2 H1 GLU 1 -20.871 8.447 -5.051 1.00 0.00
> ATOM 3 H2 GLU 1 -19.241 8.579 -5.199 1.00 0.00
> ATOM 4 H3 GLU 1 -20.238 9.911 -4.660 1.00 0.00
> ATOM 5 CA GLU 1 -19.847 8.507 -3.304 1.00 0.00
> ATOM 6 HA GLU 1 -18.845 8.057 -3.227 1.00 0.00
> ATOM 7 CB GLU 1 -19.913 9.782 -2.416 1.00 0.00
> ATOM 8 2HB GLU 1 -20.026 9.493 -1.358 1.00 0.00
> ATOM 9 3HB GLU 1 -20.055 9.447 -1.389 1.00 0.00
> ATOM 10 CG GLU 1 -18.641 10.678 -2.498 1.00 0.00
> ATOM 11 2HG GLU 1 -18.628 11.255 -3.435 1.00 0.00
> ATOM 12 3HG GLU 1 -19.554 10.087 -2.431 1.00 0.00
> ATOM 13 CD GLU 1 -18.573 11.627 -1.334 1.00 0.00
> ATOM 14 OE1 GLU 1 -19.009 12.797 -1.488 1.00 0.00
> ATOM 15 OE2 GLU 1 -18.089 11.174 -0.257 1.00 0.00
> ATOM 16 C GLU 1 -20.807 7.451 -2.751 1.00 0.00
> ATOM 17 O GLU 1 -21.843 7.183 -3.340 1.00 0.00

The above look like Amber names, formatted according to the old (version 2)
pdb format. Amber should be able to read such a file correctly. [To convert
to the current Amber/PDB (version 3) format, change "2HB " to " HB2", etc.]

> ATOM 18 1HB GLU 1 -20.805 10.368 -2.695 1.00 0.00
> ATOM 19 1HG GLU 1 -17.724 10.072 -2.453 1.00 0.00
> ATOM 20 2HT GLU 1 -19.381 9.526 -5.140 1.00 0.00
> ATOM 21 1HT GLU 1 -20.892 8.644 -5.172 1.00 0.00

The atoms above are incorrect: the PDB used to have atoms like "1HB", but
no longer does so. The HT1,HT2 pair looks somehow like a neutral N-terminal
amino acid: by default, Amber treats an N-terminal residue as positively
charged. In any event, you could not have both the first 17 atoms *and* the
last 4 in the same residue.

> These are the GLU 1 atoms after adding H

...[omitted]...

I'm out of my league here, since I don't know what program was used here, or
with what input. Nor do I know what gromacs wants. The current AmberTools
follows the PDB standard (version 3) very closely for proteins, and that will
also soon be the case for nucleic acids as well.

I hope this provides some help; not all that confident, however.

...dac

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