[gmx-developers] missing atoms in pdb2gmx

Berk Hess gmx3 at hotmail.com
Wed Apr 10 18:21:45 CEST 2002


We just found out that pdb2gmx can generate an incomplete topology
without giving any warnings. If an H or an O atom is missing in the
pdb file, pdb2gmx will generate a topology without this missing atom,
which is, of course, very bad.
This problem can occur easily when a user adds a residue to the
database, but forgets to add it to the hydrogen database. So I think
several users might have performed incorrect simulations without
For all the standard residues there is no problem.

I removed the check on H and O, so pdb2gmx now always generates a
warning and gives a fatal error, unless the new option -missing is

For a missing atom with name H* or h* the warning now is:

WARNING: atom H is missing in residue GLU 32 in the pdb file
         You might need to add atom H to the hydrogen database of residue 
         in the file ff???.hdb (see the manual)

The fatal error is:

Fatal error: There were 9 missing atoms in molecule Protein, if you want to 
use this incomplete topology anyhow, use the option -missing

If there are no objections I'll commit these changes.


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