[gmx-users] "Missing" water hydrogens

Alan Dodd anoddlad at yahoo.com
Fri Jan 7 15:46:42 CET 2005

When trying to create an appropriate .gro and .top
file using pdb2gmx with -ignh, I keep getting the
following error:
WARNING: atom HW3 is missing in residue HOH 4798 in
the pdb file
         You might need to add atom HW3 to the
hydrogen database of residue HOH
         in the file ff???.hdb (see the manual)
For all the waters in the PDB. All hydrogens are
present and correct:

ATOM  20302  OW  SOL   4798      64.970  63.060  
7.780  1.00  0.00
ATOM  20303  HW1 SOL   4798      65.362  63.882  
7.368  1.00  0.00
ATOM  20304  HW2 SOL   4798      65.492  62.259  
7.489  1.00  0.00

Using -missing allows an output to be created, but why
on earth is GROMACS trying to put in an extra
hydrogen?  The output files also register a massively
positive (over 5000) charge for the system -
presumably due to all the protonated waters that are
now present (although not in the output .gro file)? 
How can I get rid of this?  

Thanks for your time.

Alan Dodd
University of Bristol

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