Does the atom2cg_v2.1.awk require the indication of the subunit (A, B, C, etc) in the pdb file of a multimeric protein?
From ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00 C ATOM 3 CB LEU 1 155.257 66.191 95.767 0.00 0.00 C ATOM 4 CG LEU 1 156.589 66.550 95.065 0.00 0.00 C ATOM 5 CD1 LEU 1 156.406 66.834 93.574 0.00 0.00 C ATOM 6 CD2 LEU 1 157.222 67.770 95.727 0.00 0.00 C ATOM 7 C LEU 1 155.425 63.717 95.081 0.00 0.00 C ATOM 8 O LEU 1 155.371 63.026 94.063 0.00 0.00 O ATOM 9 N SER 2 156.233 63.409 96.105 0.00 0.00 N I get ATOM 2 BN0 LEU 154.534 64.963 95.169 0.000 0.00 0.00 ATOM 4 SC1 LEU 156.589 66.550 95.065 0.000 0.00 0.00 ATOM 10 BN0 SER 157.124 62.235 96.094 0.000 0.00 0.00 i.e., weird residue numbers. In another case (coming from AMBER, where the subunit indication is omitted) with the subunit indicated, the residue numbers in the cg file are correct. I don't see any other difference between the two starting files. Or should I look for a different cause. thanks francesco pietra ....... -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
