[gmx-users] Pdb2gmx and tip4p dummy atom position

[TJ Piggot]

Dear Gromacs Users,

I have used pdb2gmx to convert my pdb, containing protein and 
crystallographic waters, to obtain .gro and .top files using the following 
command:

pdb2gmx -f foo.pdb -water tip4p -ff oplsaa

There is no error from pdb2gmx, however the dummy atom (MW/HW3) from the 
crystallographic tip4p waters (added by pdb2gmx) has the same co-ordinates 
as the oxygen atom (OW), leading to short bond warnings produced by 
pdb2gmx, for example:

Warning: Short Bond (1613-1616 = 0 nm)

This has been reported on the list before however i have not found a way to 
alter the position at which pdb2gmx places the dummy atom so as to be in 
the same orientation as in the tip4p.gro file.

Despite these short bond warnings i can continue in the usual manner 
(editconf, genbox, grompp, mdrun) without any further warnings.

If anyone can help with how to alter the position at which pdb2gmx places 
the dummy atom it would be much appreciated, or is it better to ignore the 
warnings and to equilibrate for longer than normal to try and resolve the 
problem?

Tom Piggot

----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.