[gmx-users] "Missing" water hydrogens
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
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.
University of Bristol
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