[gmx-users] Crystallographic waters for TIP4P

Choon Peng cpchng at bii.a-star.edu.sg
Sun Jul 25 10:37:21 CEST 2004

Dear users,

  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

I get:
    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
bulk solvent.
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?
Making bonds...
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
Research Associate
Computational Biology Group
BioInformatics Institute, BMSI
30 Biopolis Street, #07-01 Matrix, Singapore 138671.

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