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AMBER Archive (2007)Subject: RE: AMBER: Missplaced TERs
From: Steve Seibold (seibold_at_chemistry.msu.edu)
Sorry Dave. I was not clear. The previous files I sent you were the
Steve
MINE: For the two copper metals:
ATOM 4319 CE3 TRP A 560 -47.015 194.172 -10.040 41.81
ATOM 4320 CZ2 TRP A 560 -44.542 195.531 -10.061 42.51
ATOM 4321 CZ3 TRP A 560 -46.157 194.065 -11.148 40.90
ATOM 4322 CH2 TRP A 560 -44.933 194.756 -11.164 41.03
ATOM 4323 OXT TRP A 560 -49.710 198.090 -7.649 0.00
TER 4324 TRP A 560
ATOM 4325 N LEU B 30 -29.457 145.279 43.045 57.47
ATOM 4326 CA LEU B 30 -29.433 145.898 41.698 57.86
ATOM 4327 C LEU B 30 -30.849 146.305 41.259 57.86
ATOM 6367 CG LEU B 289 -23.957 140.880 37.319 51.97
ATOM 8508 OE1 GLN C 266 -6.030 156.308 -16.837 57.11
MINE: For the Three copper metals:
ATOM 4320 CZ2 TRP A 560 -44.542 195.531 -10.061 42.51
ATOM 8509 NE2 GLN C 266 -6.378 154.539 -15.528 55.98
-----Original Message-----
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
> of the misplacement of "TER" comes when I have water AND when I have
> 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
> 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
after OXT of GLN 1072. Could you try adding this to see if that helps?
....good luck...dac
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