[gmx-users] Fatal Error: Water molecule
Amol D. Atre
ssb4 at udct.org
Sat Oct 1 09:15:50 CEST 2005
Trying to generate topology for a single molecule of water. PDB file looks
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.
Chemical Engineering Department,
Mumbai University Institute of Chemical Technology,
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