[gmx-users] Pdb2gmx and tip4p dummy atom position

[TJ Piggot]

Great, thanks for the answer

Tom

--On Friday, May 30, 2008 17:22:46 +0200 David van der Spoel 
<spoel at xray.bmc.uu.se> wrote:

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