[gmx-users] Crystallographic waters for TIP4P
cpchng at bii.a-star.edu.sg
Sun Jul 25 10:37:21 CEST 2004
I'm having trouble getting crystallographic waters contained in the PDB
file to be converted into TIP4P waters.
Trying to use OPLS-AA/L force-field with TIP4P waters.
Seems no problem if we have bulk solvent only.
>From the O atom in the PDB file, say:
HETATM 457 O HOH 59 1.499 -5.556 1.019 1.00 1.60
1HO4 OW 1 0.150 -0.556 0.102
1HO4 HW1 2 0.232 -0.556 0.160
1HO4 HW2 3 0.068 -0.556 0.160
1HO4 HW3 4 0.150 -0.556 0.102
using Gromacs 3.2.1 with "-water tip4p" option.
This seems to be in the wrong format, as TIP4P waters have entries
MW1,HW2,HW3,OW4 (MW1 is the 4th site).
Genbox then ignores these waters and generates 3 extra TIP4P waters in the
The same problem was encountered by Sunita in:
but no satisfactory answers were given.
Has it to do with the following error when we run pdb2gmx?
Warning: Short Bond (1-4 = 0 nm)
Warning: Short Bond (5-8 = 0 nm)
Warning: Short Bond (9-12 = 0 nm)
And when i decide to try TIP3P instead, tip3p.gro is not in the
distribution though tip3p is an option to "-water".
Any help is appreciated.
Thank you very much.
Mr. Choon-Peng CHNG
Computational Biology Group
BioInformatics Institute, BMSI
30 Biopolis Street, #07-01 Matrix, Singapore 138671.
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