[gmx-users] ATP

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 20 11:27:01 CEST 2003

On Fri, 2003-06-20 at 21:07, Kay Gottschalk wrote:
> Hi there,
> my system is a protein with ATP, and I'm using the Gromacs ff. In the 
> initial pdb-file, 3 hydrogens are missing, thus Gromacs nicely 
> complains about that. If I just leave them out (with the '-missing' 
> option), ATP is too negatively charged. Is there any reasonable way to 
> build the hydrogens with Gromacs? Unfortunately I don't have Insight 
> here, and SwissPDB cannot do it. Alternatively I might increase the 
> radius and weight and decrease the charge of the affected oxygens in 
> the sense of a 'united atoms ATP', but I'd rather avoid that (the 
> dipoles just would be fucked up, and h-bonds will not be able to 
> form... ). Help would be appreciated.
you may be able to do it in two steps, since the ATP is not covalently
Cut out the ATP from your pdb file into another and run pdb2gmx on each.
Then merge them manually.
> Thanks a lot,
> Kay.
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David van der Spoel <spoel at xray.bmc.uu.se>

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