[gmx-users] Fatal Error: Water molecule

Amol D. Atre ssb4 at udct.org
Sat Oct 1 09:15:50 CEST 2005

Hello all,

Trying to generate topology for a single molecule of water. PDB file looks
like following,

ATOM      1  OW    SOL     1      -0.026  -0.365   0.000  1.00  0.00
ATOM      2  HW1   SOL     1      -0.761   0.237   0.000  1.00  0.00
ATOM      3  HW2   SOL     1       0.787   0.127   0.000  1.00  0.00

Command line: pdb2gmx -f Water.pdb -o conf.gro -p topol.top

Warning: 'SO' not found in residue topology database, trying to use 'SO42-'
Fatal error: Atom OW in residue SO42- 1 not found in rtp entry with 5 atoms
             while sorting atoms

What could be the possible reason for this? How can this problem be solved?

My OS is PCQ Linux 2004.

Thanking in advance.

Amol D. Atre.
Lab No.A002,
Chemical Engineering Department,
Mumbai University Institute of Chemical Technology,
Matunga(E), Mumbai-400019.

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