Martinize2 can not separate my protein chains... #73
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MarcosAR94
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Hi! Looking for human advice
I'm working with a homopentameric transmembrane protein following the tutorial, and I'm stuck at the CG conversion. Martinize2 is outputting my last 2 chains into the same itp file
having a molecule_0.itp, 1, 2 and what should be 3 and 4 is integrated into the same
I have already set a letter for each corresponding chain
having TER terms between the last and first amino acid residues when a new chain begins
and each residue has its own residue number, instead of having a repeating sequence of 340 numbers.
Issue here
ATOM 21821 1HB HIS D1360 106.637 -27.493 71.575 1.00 0.00 HATOM 21822 2HB HIS D1360 106.724 -26.417 70.171 1.00 0.00 HATOM 21823 HD2 HIS D1360 108.013 -26.687 73.786 1.00 0.00 HATOM 21824 HE1 HIS D1360 109.559 -23.104 72.248 1.00 0.00 HTERATOM 21825 N GLY E1361 107.253 33.773 56.330 1.00 11.63 NATOM 21826 CA GLY E1361 108.310 33.237 55.442 1.00 11.63 CATOM 21827 C GLY E1361 107.701 32.457 54.324 1.00 11.63 CATOM 21828 O GLY E1361 107.470 32.988 53.239 1.00 11.63 OThis is the current output (the last part without the citations reminder anyway)
DEBUG - step - vermouth - Writing molecule molecule_0 with 828 atoms, 900 edges, 340 position_restraints, 907 bonds, 447 constraints, 1435 angles, 444 dihedrals, 188 exclusions, 26 impropers, and 6 virtual_sitesn.
INFO - model - vermouth - Disulfide bridge found between residues A-CYS131 and A-CYS145
DEBUG - step - vermouth - Writing molecule molecule_1 with 828 atoms, 900 edges, 340 position_restraints, 908 bonds, 446 constraints, 1435 angles, 443 dihedrals, 188 exclusions, 26 impropers, and 6 virtual_sitesn.
INFO - model - vermouth - Disulfide bridge found between residues B-CYS131 and B-CYS145
DEBUG - step - vermouth - Writing molecule molecule_2 with 828 atoms, 900 edges, 340 position_restraints, 908 bonds, 446 constraints, 1435 angles, 443 dihedrals, 188 exclusions, 26 impropers, and 6 virtual_sitesn.
INFO - model - vermouth - Disulfide bridge found between residues C-CYS131 and C-CYS145
DEBUG - step - vermouth - Writing molecule molecule_3 with 1656 atoms, 1801 edges, 680 position_restraints, 1815 bonds, 893 constraints, 2870 angles, 887 dihedrals, 376 exclusions, 52 impropers, and 12 virtual_sitesn.
INFO - model - vermouth - Disulfide bridge found between residues D-CYS131 and D-CYS145
INFO - model - vermouth - Disulfide bridge found between residues E-CYS471 and E-CYS485
INFO - general - vermouth.processors.quote - Happiness is a dry martini and a good woman... or a bad woman. -- George Burns
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