On 26/02/2012 10:08 PM, shilpa yadahalli wrote:
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)
pdb2gmx TIP4P support for CHARMM was mysteriously removed shortly before
4.5.2 in commit 73b6d63
You can try adding the following to your aminoacids.rtp
Mark
[ HO4 ]
; TIP4P
[ atoms ]
OW OWT4 0.00 0
HW1 HWT4 0.52 0
HW2 HWT4 0.52 0
MW MWT4 -1.04 0
[ bonds ]
OW HW1
OW HW2
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