[gmx-developers] Suggestion : hydrogen generation

Michel Cuendet michel.cuendet at isb-sib.ch
Thu Aug 6 16:53:42 CEST 2009

Thanks David for your reply.

I would be interested to try your toolkit, although I already have a 
workaround using either charmm or pdb2pqr. I think that as far as the 
construction of hydrogens is concerned, the details of which forcefield 
you use are quite secondary. An ad-hoc hydrogen bond scoring function 
might even do the trick.

The point of my massage was to report a case where the restrained 
equilibration does not make up for bad initial hydrogen placement. Of 
course, users who want fancy pKa based protonations, Asn and Gln 
flipping, Monte Carlo interdependent optimization, etc... use other 
tools. But less experienced users who simply run the gromacs setup 
pipeline on a pdb file are at risk of getting bad results... I therefore 
think it would be good if a minimal optimization stage was done in 
directly pdb2gmx.

Can you send me a link to your toolkit off-list?

> Message: 4
> Date: Thu, 6 Aug 2009 08:48:28 -0500
> From: David Mobley <dmobley at gmail.com>
> Subject: Re: [gmx-developers] Suggestion : hydrogen generation
> To: Discussion list for GROMACS development
> 	<gmx-developers at gromacs.org>
> Message-ID: <2A0AD657-FAA4-4DC1-9610-E62D2E8EA7B6 at gmail.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> I've got a toolkit I'm getting ready to release that does a whole  
> bunch of things; the one that pertains to this discussion is that it  
> uses MCCE to assign protonation states and add protons. The proton  
> positions and protonation states are optimized based on environment if  
> I understand correctly. It's possible it might solve your problem.  
> Unfortunately at this point it's specific for the AMBER force field,  
> though that's just an issue of residue/atom naming.
> I can give you access to it if you're interested in checking it out.  
> The reason it is not released yet is just that there's still various  
> cleaning up that I need to do, and I need to add some licensing (GPL),  
> etc.
> David Mobley, Ph.D.
> Assistant Professor of Chemistry
> University of New Orleans
> New Orleans, LA 70148
> dlmobley at uno.edu
> Phone 504-383-3662
> Fax 504-280-6860

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