[gmx-users] Pdb2gmx and tip4p dummy atom position

[David van der Spoel]

TJ Piggot wrote:
> 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?
> 
This is irrelevant, since the dummy positions are generated in mdrun.

> Tom Piggot
> 
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
> 
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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://folding.bmc.uu.se
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