AMBER Archive (2007)

Subject: Re: AMBER: Missplaced TERs

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 16 2007 - 13:53:10 CDT

On Thu, Aug 16, 2007, Steve Seibold wrote:
>
> These pdb files (below) were generated using the leap.in I am sending
> you. I removed the water and sections to make them smaller. The problem
> of the misplacement of "TER" comes when I have water AND when I have my
> three metals present. If I only have two metals the "TER"s are placed
> correctly (see TWO.CU.nw.pdb below). The file THREE.CU.nw.pdb (also
> below) was made in an identical manner as TWO.CU.nw.pdb except that the
> third metal (CUB) was added and this causes the misplacement of "TER".

> TWO.CU.nw.pdb File:
>
>
> ATOM 16820 NE2 GLN 1072 72.247 30.758 37.407
> ATOM 16821 1HE2 GLN 1072 71.246 30.835 37.301
> ATOM 16822 2HE2 GLN 1072 72.647 30.020 37.969
> ATOM 16823 C GLN 1072 74.323 30.303 40.060
> ATOM 16824 O GLN 1072 74.755 30.057 41.212
> ATOM 16825 OXT GLN 1072 73.892 29.455 39.244
> TER
> ATOM 16826 CU CUA 1073 48.484 24.911 66.640
> TER
> ATOM 16827 CU CUA 1074 50.415 23.216 67.258
> END

Note that the above file (which "works") correctly has a TER card after
the OXT of GLN 1072.

>
> THREE.CU.nw.pdb File (below)
>
>
> ATOM 16823 C GLN 1072 74.323 30.303 40.060
> ATOM 16824 O GLN 1072 74.755 30.057 41.212
> ATOM 16825 OXT GLN 1072 73.892 29.455 39.244
> ATOM 16826 CU CUA 1073 48.484 24.911 66.640
> TER
> ATOM 16827 CU CUA 1074 50.415 23.216 67.258
> TER
> ATOM 16828 CU CUB 1075 48.175 45.879 60.797
> END

The above file (which, as I understand it, fails), is missing the TER card
after OXT of GLN 1072. Could you try adding this to see if that helps?

....good luck...dac

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