Hello Charles and other members of Xplor-NIH,
I am attempting to calculate a structure of a heterodimer/complex consisting of
a small peptide bound to a protein using Xplor-NIH and primarily NOE
restraints. I am however experiencing some difficulties in providing a correct
psf and/or pdb input (it appears). All of my attempts end up with an all
"unknown atomic coordinates" error (details below), although the calculation
finishes without "irregular exit" (but with a senseless result). The two
proteins are described in a single psf and pdb file, with segid A and B.
Can anyone help me figure out the problem, or point me in the right
direction(s)?
Thanks in advance.
Best regards,
Katrine
Region of Refine.py script for reading psf and pdb:
import protocol
protocol.initRandomSeed(3421)
command = xplor.command
protocol.initParams("protein")
protocol.initStruct("xComplex.psf")
protocol.loadPDB("xcomplex.pdb")
xplor.simulation.deleteAtoms("not known")
protocol.updatePseudoAtoms()
protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
Resulting in the followin output message:
refine.py(49): protocol.initStruct("xComplex.psf")
X-PLOR>struct reset end
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 0(MAXA= 200) NBOND= 0(MAXB= 0)
NTHETA= 0(MAXT= 0) NGRP= 0(MAXGRP= 0)
NPHI= 0(MAXP= 0) NIMPHI= 0(MAXIMP= 0)
NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0)
NNB= 0(MAXNB= 0)
X-PLOR>end
X-PLOR>struct @xComplex.psf end
ASSFIL: file
/--/--/Data/NMR/--/Structure_calculations/XPLOR-NIH/--/--/xComplex.psf opened.
STRUcture>PSF
REMARKS FILENAME="/--/--/Data/NMR/--/--/X"
REMARKS TOPH11-MACRO for protein sequence
REMARKS DATE: 6-Oct-16 14:21:54 created by user: twv382
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 1509(MAXA= 1600) NBOND= 1520(MAXB= 1600)
NTHETA= 2756(MAXT= 3200) NGRP= 625(MAXGRP= 800)
NPHI= 181(MAXP= 200) NIMPHI= 764(MAXIMP= 800)
NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100)
NNB= 558(MAXNB= 800)
STRUcture> end
X-PLOR>end
refineKB_RSTdreb.py(62): protocol.loadPDB("xcomplex.pdb")
loading pdb file: xcomplex.pdb [psf] initCoords: still 1509 unknown atomic
coordinates
[coords]
refine.py(64): xplor.simulation.deleteAtoms("not known")
MAPIC: Atom numbers being modified
refine.py(66): protocol.updatePseudoAtoms()
refine.py(68): protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
Example of parts of the generated psf (protein A: res 498-572, protein B: res
255-272):
1509 !NATOM
1 A 498 MET N NH3 -0.100000 14.0070 0
2 A 498 MET HT1 HC 0.260000 1.00800 0
3 A 498 MET HT2 HC 0.260000 1.00800 0
4 A 498 MET HT3 HC 0.260000 1.00800 0
5 A 498 MET CA CT 0.220000 12.0110 0
6 A 498 MET HA HA 0.100000 1.00800 0
7 A 498 MET CB CT -0.200000 12.0110 0
8 A 498 MET HB1 HA 0.100000 1.00800 0
...(etc etc)
...
1238 A 572 SER OG OH -0.680000 15.9990 0
1239 A 572 SER HG H 0.400000 1.00800 0
1240 A 572 SER C C 0.140000 12.0110 0
1241 A 572 SER OT1 OC -0.570000 15.9990 0
1242 A 572 SER OT2 OC -0.570000 15.9990 0
1243 B 255 SER N NH3 -0.100000 14.0070 0
1244 B 255 SER HT1 HC 0.260000 1.00800 0
1245 B 255 SER HT2 HC 0.260000 1.00800 0
1246 B 255 SER HT3 HC 0.260000 1.00800 0
1247 B 255 SER CA CT 0.220000 12.0110 0
1248 B 255 SER HA HA 0.100000 1.00800 0
1249 B 255 SER CB CT 0.800000E-01 12.0110 0
1250 B 255 SER HB1 HA 0.100000 1.00800 0
1251 B 255 SER HB2 HA 0.100000 1.00800 0
1252 B 255 SER OG OH -0.680000 15.9990 0
1253 B 255 SER HG H 0.400000 1.00800 0
1254 B 255 SER C C 0.480000 12.0110 0
1255 B 255 SER O O -0.480000 15.9990 0
1256 B 256 SER N NH1 -0.360000 14.0070 0
1257 B 256 SER HN H 0.260000 1.00800 0
1258 B 256 SER CA CT 0.00000 12.0110 0
1259 B 256 SER HA HA 0.100000 1.00800 0
...(etc etc)
...
Example of parts of the generated pdb:
ATOM 1 N MET A 498 -4.545 -0.208 -0.063 1.00 0.00
ATOM 2 HT1 MET A 498 -4.241 -0.222 0.930 1.00 0.00
ATOM 3 HT2 MET A 498 -5.420 -0.762 -0.168 1.00 0.00
ATOM 4 HT3 MET A 498 -4.719 0.774 -0.356 1.00 0.00
ATOM 5 CA MET A 498 -3.479 -0.800 -0.920 1.00 0.00
ATOM 6 HA MET A 498 -3.836 -1.725 -1.349 1.00 0.00
ATOM 7 CB MET A 498 -3.130 0.180 -2.042 1.00 0.00
ATOM 8 HB1 MET A 498 -2.255 0.748 -1.766 1.00 0.00
ATOM 9 HB2 MET A 498 -3.960 0.852 -2.203 1.00 0.00
ATOM 10 CG MET A 498 -2.845 -0.597 -3.329 1.00 0.00
ATOM 11 HG1 MET A 498 -3.452 -0.202 -4.130 1.00 0.00
ATOM 12 HG2 MET A 498 -3.082 -1.640 -3.180 1.00 0.00
ATOM 13 SD MET A 498 -1.095 -0.431 -3.760 1.00 0.00
ATOM 14 CE MET A 498 -0.549 0.320 -2.206 1.00 0.00
ATOM 15 HE1 MET A 498 0.525 0.443 -2.225 1.00 0.00
ATOM 16 HE2 MET A 498 -0.821 -0.319 -1.381 1.00 0.00
ATOM 17 HE3 MET A 498 -1.026 1.283 -2.086 1.00 0.00
ATOM 18 C MET A 498 -2.243 -1.080 -0.070 1.00 0.00
ATOM 19 O MET A 498 -2.255 -1.964 0.787 1.00 0.00
ATOM 20 N SER A 499 -1.179 -0.322 -0.314 1.00 0.00
ATOM 21 HN SER A 499 -1.227 0.367 -1.009 1.00 0.00
ATOM 22 CA SER A 499 0.060 -0.498 0.436 1.00 0.00
...(etc etc)
...
ATOM 1233 CA SER A 572 127.327 -0.270 -1.927 1.00 0.00
ATOM 1234 HA SER A 572 128.094 0.205 -1.334 1.00 0.00
ATOM 1235 CB SER A 572 127.156 -1.711 -1.448 1.00 0.00
ATOM 1236 HB1 SER A 572 127.919 -1.939 -0.716 1.00 0.00
ATOM 1237 HB2 SER A 572 127.251 -2.384 -2.284 1.00 0.00
ATOM 1238 OG SER A 572 125.866 -1.863 -0.871 1.00 0.00
ATOM 1239 HG SER A 572 125.947 -2.447 -0.113 1.00 0.00
ATOM 1240 C SER A 572 127.758 -0.264 -3.390 1.00 0.00
ATOM 1241 OT1 SER A 572 127.156 0.464 -4.162 1.00 0.00
ATOM 1242 OT2 SER A 572 128.684 -0.988 -3.717 1.00 0.00
ATOM 1243 N SER B 255 118.841 -1.290 0.671 1.00 0.00
ATOM 1244 HT1 SER B 255 118.514 -1.253 1.657 1.00 0.00
ATOM 1245 HT2 SER B 255 118.090 -1.685 0.070 1.00 0.00
ATOM 1246 HT3 SER B 255 119.075 -0.330 0.350 1.00 0.00
ATOM 1247 CA SER B 255 120.052 -2.154 0.582 1.00 0.00
ATOM 1248 HA SER B 255 120.486 -2.266 1.564 1.00 0.00
ATOM 1249 CB SER B 255 119.655 -3.529 0.042 1.00 0.00
ATOM 1250 HB1 SER B 255 118.828 -3.917 0.622 1.00 0.00
...(etc etc)
...
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