Dear gmx-users,
I am using CHARMM27 all-atom force field (with CMAP) - version 2.0 force field with gromacs 4.5.2 version. I want to retain my crystal waters in pdb file. I wrote crystal water according to the same convention when gromacs solvates protein molecule. last pat of pdb looks like: ATOM 1459 CA LEU A 94 9.264 -6.783 6.273 0.0700 2.2750 ATOM 1460 C LEU A 94 9.604 -7.603 5.021 0.3400 2.0000 ATOM 1461 OT1 LEU A 94 10.488 -7.171 4.243 -0.6700 1.7000 ATOM 1462 CB LEU A 94 9.865 -7.422 7.524 -0.1800 2.1750 ATOM 1463 CG LEU A 94 11.295 -7.028 7.888 -0.0900 2.2750 ATOM 1464 CD1 LEU A 94 11.525 -5.554 7.645 -0.2700 2.0600 ATOM 1465 CD2 LEU A 94 11.541 -7.378 9.338 -0.2700 2.0600 ATOM 1466 OT2 LEU A 94 9.160 -8.652 4.607 -0.6700 1.7000 ATOM 1478 OW SOL A 95 10.102 -4.251 13.943 -0.8340 1.7682 ATOM 1479 HW1 SOL A 95 11.032 -3.906 14.073 0.4170 0.2245 ATOM 1480 HW2 SOL A 95 9.584 -4.002 14.761 0.4170 0.2245 ATOM 1481 OW SOL A 96 1.041 -4.800 4.090 -0.8340 1.7682 ATOM 1482 HW1 SOL A 96 0.661 -4.642 5.002 0.4170 0.2245 ATOM 1483 HW2 SOL A 96 1.894 -4.299 3.947 0.4170 0.2245 ATOM 1484 OW SOL A 97 -0.433 3.575 23.826 -0.8340 1.7682 ATOM 1485 HW1 SOL A 97 0.247 2.969 23.412 0.4170 0.2245 ATOM 1486 HW2 SOL A 97 -1.278 3.091 24.054 0.4170 0.2245 I used reference (http://pubs.acs.org/doi/full/10.1021/ct900549r ) that its better to use TIP4-point water model with CHARMM. But it gives me following fatal error: Residue 'HO4' not found in residue topology database But there is not such atom in my input file. I do not get such error if I'm using TIP3P water model. Also, If i delete crystal water molecules, and use TIP4P, then it doens't give me any error (but i dnt water to delete crystal water molecule) Can anyone please guide/comment regarding. Thanks alot, Shilpa
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