[gmx-users] editconf errors for isoleucine residue
YOLANDA SMALL
yas102 at psu.edu
Thu Apr 21 04:59:06 CEST 2005
Hello,
I used the editconf utility to convert a file from pdb to gro and back to pdb
again. There appears to be an error in converting the units and it only
happens with the isoleucine residue on a 365 residue protein. The .gro file is
using the digits after the decimal so perhaps the unit conversion part of the
code is malfunctioning. I have attached the section of the files for you to
see. Is this a known problem? Has anyone else encounterd this problem? Is there
a fix for it?
Thanks,
Yolanda
>From original pdb file
ATOM 1370 N ILE A 89 48.865 40.003 13.593 1.00 0.00
ATOM 1371 CA ILE A 89 49.550 38.952 12.846 1.00 0.00
ATOM 1372 C ILE A 89 48.833 37.610 13.056 1.00 0.00
ATOM 1373 O ILE A 89 48.208 37.380 14.095 1.00 0.00
ATOM 1374 CB ILE A 89 51.052 38.899 13.240 1.00 0.00
ATOM 1375 CG1 ILE A 89 51.329 38.529 14.720 1.00 0.00
ATOM 1376 CG2 ILE A 89 51.766 40.205 12.847 1.00 0.00
ATOM 1377 CD ILE A 89 52.802 38.195 14.994 1.00 0.00
ATOM 1378 H ILE A 89 48.697 39.833 14.579 1.00 0.00
ATOM 1379 HA ILE A 89 49.487 39.162 11.777 1.00 0.00
ATOM 1380 HB ILE A 89 51.492 38.112 12.623 1.00 0.00
ATOM 1381 HG11 ILE A 89 51.006 39.339 15.376 1.00 0.00
ATOM 1382 HG12 ILE A 89 50.739 37.661 15.013 1.00 0.00
ATOM 1383 HG21 ILE A 89 52.840 40.052 12.752 1.00 0.00
ATOM 1384 HG22 ILE A 89 51.410 40.580 11.889 1.00 0.00
ATOM 1385 HG23 ILE A 89 51.590 40.992 13.581 1.00 0.00
ATOM 1386 HD1 ILE A 89 53.157 37.399 14.339 1.00 0.00
ATOM 1387 HD2 ILE A 89 53.444 39.064 14.848 1.00 0.00
ATOM 1388 HD3 ILE A 89 52.934 37.859 16.021 1.00 0.00
Gro file generated with (editconf -f file.pdb -o file1.gro)
89ILE N 1371 86.500 0.300 59.300
89ILE H 1372 69.700 83.300 57.900
89ILE CA 1373 55.000 95.200 84.600
89ILE HA 1374 48.700 16.200 77.700
89ILE CB 1375 5.200 89.900 24.000
89ILE HB 1376 49.200 11.200 62.300
89ILE CG1 1377 32.900 52.900 72.000
89ILE HG11 1378 0.600 33.900 37.600
89ILE HG12 1379 73.900 66.100 1.300
89ILE CG2 1380 76.600 20.500 84.700
89ILE HG21 1381 84.000 5.200 75.200
89ILE HG22 1382 41.000 58.000 88.900
89ILE HG23 1383 59.000 99.200 58.100
89ILE CD 1384 80.200 19.500 99.400
89ILE HD1 1385 15.700 39.900 33.900
89ILE HD2 1386 44.400 6.400 84.800
89ILE HD3 1387 93.400 85.900 2.100
89ILE C 1388 83.300 61.000 5.600
89ILE O 1389 20.800 38.000 9.500
PDB file generated with (editconf -f file1.gro -o file2.pdb)
ATOM 1371 N ILE 89 865.000 3.000 593.000 1.00 0.00
ATOM 1372 H ILE 89 697.000 833.000 579.000 1.00 0.00
ATOM 1373 CA ILE 89 550.000 952.000 846.000 1.00 0.00
ATOM 1374 HA ILE 89 487.000 162.000 777.000 1.00 0.00
ATOM 1375 CB ILE 89 52.000 899.000 240.000 1.00 0.00
ATOM 1376 HB ILE 89 492.000 112.000 623.000 1.00 0.00
ATOM 1377 CG1 ILE 89 329.000 529.000 720.000 1.00 0.00
ATOM 1378 HG11 ILE 89 6.000 339.000 376.000 1.00 0.00
ATOM 1379 HG12 ILE 89 739.000 661.000 13.000 1.00 0.00
ATOM 1380 CG2 ILE 89 766.000 205.000 847.000 1.00 0.00
ATOM 1381 HG21 ILE 89 840.000 52.000 752.000 1.00 0.00
ATOM 1382 HG22 ILE 89 410.000 580.000 889.000 1.00 0.00
ATOM 1383 HG23 ILE 89 590.000 992.000 581.000 1.00 0.00
ATOM 1384 CD ILE 89 802.000 195.000 994.000 1.00 0.00
ATOM 1385 HD1 ILE 89 157.000 399.000 339.000 1.00 0.00
ATOM 1386 HD2 ILE 89 444.000 64.000 848.000 1.00 0.00
ATOM 1387 HD3 ILE 89 934.000 859.000 21.000 1.00 0.00
ATOM 1388 C ILE 89 833.000 610.000 56.000 1.00 0.00
ATOM 1389 O ILE 89 208.000 380.000 95.000 1.00 0.00
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