AMBER Archive (2007)

Subject: RE: AMBER: Missplaced TERs

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Aug 16 2007 - 14:47:38 CDT

Sorry Dave. I was not clear. The previous files I sent you were the
"output" files written by the module ambpdb of Sander with the misplaced
TERs. My "input" pdb files with what I think are the correct placement
of TERS are shown below. Basically when I add the third metal CUB with
waters I get the misplaced TERS as shown in previous email. The systems
admin did increase the number of atoms/residues accepted by ambpdb and
recompiled the system, but he is very good and I doubt that he did
something to cause this. But if he could have caused this, what should
he look for in the ambpdb script? What is also very strange is that if I
save the three OR the two copper system in xleap (i.e using savePdb file
file.pdb) I again get a misplacement of a TER command, but in a
different location. Would it be better to send you my leap.log files for
these situations?

 

Steve

 

MINE: For the two copper metals:

 

ATOM 4319 CE3 TRP A 560 -47.015 194.172 -10.040 41.81
C

ATOM 4320 CZ2 TRP A 560 -44.542 195.531 -10.061 42.51
C

ATOM 4321 CZ3 TRP A 560 -46.157 194.065 -11.148 40.90
C

ATOM 4322 CH2 TRP A 560 -44.933 194.756 -11.164 41.03
C

ATOM 4323 OXT TRP A 560 -49.710 198.090 -7.649 0.00
O1-

TER 4324 TRP A 560

ATOM 4325 N LEU B 30 -29.457 145.279 43.045 57.47
N

ATOM 4326 CA LEU B 30 -29.433 145.898 41.698 57.86
C

ATOM 4327 C LEU B 30 -30.849 146.305 41.259 57.86
C

ATOM 6367 CG LEU B 289 -23.957 140.880 37.319 51.97
C
ATOM 6368 CD1 LEU B 289 -24.785 140.346 38.498 50.96
C
ATOM 6369 CD2 LEU B 289 -22.556 141.232 37.840 51.12
C
ATOM 6370 OXT LEU B 289 -26.694 141.172 35.837 57.47
O1-
TER 6371 LEU B 289
ATOM 6372 N ALA C 2 -53.793 181.819 -25.977 72.26
N
ATOM 6373 CA ALA C 2 -53.093 182.636 -27.003 72.71
C
ATOM 6374 C ALA C 2 -53.515 182.297 -28.439 72.35
C

ATOM 8508 OE1 GLN C 266 -6.030 156.308 -16.837 57.11
O
ATOM 8509 NE2 GLN C 266 -6.378 154.539 -15.528 55.98
N
ATOM 8510 OXT GLN C 266 -4.733 153.236 -13.691 46.41
O1-
TER 8511 GLN C 266
HETATM 8512 CU CUA 1003 -30.141 148.692 13.705 25.26
Cu
TER
HETATM 8513 CU CUA 1004 -28.210 146.997 14.323 25.79
Cu
END
 

 

MINE: For the Three copper metals:

ATOM 4320 CZ2 TRP A 560 -44.542 195.531 -10.061 42.51
C
ATOM 4321 CZ3 TRP A 560 -46.157 194.065 -11.148 40.90
C
ATOM 4322 CH2 TRP A 560 -44.933 194.756 -11.164 41.03
C
ATOM 4323 OXT TRP A 560 -49.710 198.090 -7.649 0.00
O1-
TER 4324 TRP A 560
ATOM 4325 N LEU B 30 -29.457 145.279 43.045 57.47
N
ATOM 4326 CA LEU B 30 -29.433 145.898 41.698 57.86
C
ATOM 4327 C LEU B 30 -30.849 146.305 41.259 57.86
C
ATOM 6368 CD1 LEU B 289 -24.785 140.346 38.498 50.96
C
ATOM 6369 CD2 LEU B 289 -22.556 141.232 37.840 51.12
C
ATOM 6370 OXT LEU B 289 -26.694 141.172 35.837 57.47
O1-
TER 6371 LEU B 289
ATOM 6372 N ALA C 2 -53.793 181.819 -25.977 72.26
N
ATOM 6373 CA ALA C 2 -53.093 182.636 -27.003 72.71
C
ATOM 6374 C ALA C 2 -53.515 182.297 -28.439 72.35
C
ATOM 6375 O ALA C 2 -53.962 181.185 -28.711 72.95
O

ATOM 8509 NE2 GLN C 266 -6.378 154.539 -15.528 55.98
N
ATOM 8510 OXT GLN C 266 -4.733 153.236 -13.691 46.41
O1-
TER 8511 GLN C 266
HETATM 8512 CU CUA 1003 -30.141 148.692 13.705 25.26
Cu
TER
HETATM 8513 CU CUA 1004 -28.210 146.997 14.323 25.79
Cu
TER
HETATM 8514 CU CUB 1005 -30.450 169.660 7.862 26.95
Cu
END
 

 

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Thursday, August 16, 2007 2:53 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Missplaced TERs

 

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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