Hi everyone, I'm trying to figure out the right commands for make_ndx so to generate the correct index.ndx file for g_bond analysis. From my PDB file:
ATOM 1 BN0 GGA X 1 107.255 17.133 66.368 1.00 0.00 P1 C ATOM 2 SC1 GGA X 1 110.304 14.942 66.116 1.00 0.00 P1 C ATOM 3 SC2 GGA X 1 113.632 15.318 65.904 1.00 0.00 P1 C ATOM 4 SC3 GGA X 1 114.063 12.624 65.310 1.00 0.00 P1 C ATOM 5 BN0 GGA X 2 108.171 20.156 68.028 1.00 0.00 P1 C ATOM 6 SC1 GGA X 2 109.535 18.753 71.242 1.00 0.00 P1 C ATOM 7 SC2 GGA X 2 112.445 17.547 72.396 1.00 0.00 P1 C ATOM 8 SC3 GGA X 2 111.301 16.592 74.758 1.00 0.00 P1 C ATOM 9 BN0 GGA X 3 110.843 21.726 66.258 1.00 0.00 P1 C ATOM 10 SC1 GGA X 3 111.984 24.201 68.852 1.00 0.00 P1 C ATOM 11 SC2 GGA X 3 114.049 24.264 71.496 1.00 0.00 P1 C ATOM 12 SC3 GGA X 3 113.142 26.763 72.351 1.00 0.00 P1 C ..<rest of PDB file not included>... Say I want to group together atoms SC1, SC2, and SC3 from all GGA residues in make_ndx: 0 System : 19699 atoms 1 GGA : 472 atoms 2 DRG : 324 atoms 3 W : 18669 atoms 4 ION : 234 atoms I typed in: > r GGA & t SC1 | r GGA & t SC2 | r GGA & t SC3 Found 472 atoms with residue name GGA Found 36 atoms with type SC1 Merged two groups with AND: 472 36 -> 0 Found 472 atoms with residue name GGA Merged two groups with OR: 0 472 -> 472 Found 24 atoms with type SC2 Merged two groups with AND: 472 24 -> 0 Found 472 atoms with residue name GGA Merged two groups with OR: 0 472 -> 472 Found 0 atoms with type SC3 5 GGA_&_SC1_GGA_&_SC2_GGA: 472 atoms However, make_ndx "found 0 atoms with type SC3". I'm not sure if I'm doing this correctly. If anyone has any insight, I would be most appreciative. Thanks, L
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