[gmx-users] Fatal Error: Water molecule

[David]

On Sat, 2005-10-01 at 12:45 +0530, Amol D. Atre wrote:
> 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
> END
> 
> 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

the columns are incorrect in file. remove some spaces.

> 
> What could be the possible reason for this? How can this problem be solved?
> 
> My OS is PCQ Linux 2004.
> 
> Thanking in advance.
> 
> Regards,
> Amol D. Atre.
> Lab No.A002,
> Chemical Engineering Department,
> Mumbai University Institute of Chemical Technology,
> Matunga(E), Mumbai-400019.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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