[chimera-dev] hydrogen optimization

[Eric Pettersen]

Hi Terry,
	The AddH extension is pretty simple-minded right now.  The intention for 
the current simple version was that you would take the structure with the 
added hydrogens and save it (in the 1516 release, "pdbrun nouser cat > 
filename" in the midas emulator is the only practical save method; the next 
release will have the midas emulator "write" command implemented).  You 
would then use Amber to minimize the hydrogen positions.
	Quite a laborious process, I know.
	I have been working on a smarter AddH that tries to optimize placement 
for hydrogen-bonding potential and minimize steric conflicts, but other 
projects have stolen time from this and I haven't gotten much work done on 
it recently.  Now that I know somebody cares :-), I'll make the smarter 
AddH a higher priority and try to get it into the next release.
	In the interim, my only suggestion (besides the Amber thing) is that now 
that bond rotations work, you can reduce the steric conflicts by hand by 
rotating the adjacent torsion.  The viability of this approach depends on 
what project you are working on, I suppose.
	Hope this helps a little, and let us know if you have further thoughts 
or ideas.

--Eric

On Tuesday, August 13, 2002, at 06:00 PM, Terry Downing wrote:

> Hi,
>
>   I am attempting to add hydrogens to proteins with ligands bound...I am
> using the AddH extension, which appears to add hydrogens with reasonable
> bond lengths and bond angles...However, I notice that because default
> torsion angles are being used, there are situations in which the
> cartesian coordinates of the hydrogens are not optimized and result in
> clashes...This is particularly a problem with hydrogens that are
> attached to heavy atoms that are free to rotate (ie methyl and amide
> groups)...Are there any torsion minimization protocols available where I
> can optimize the torsional angle of just the newly added hydrogens
> without changing the cartesian coordinates of the heavy atoms (allow
> them to rotate to optimize the hydrogen placement but not move away from
> the experimental coordinates)?...I just spoke with Tom Ferrin and he
> said that Eric was the person most experienced with the AddH extension,
> and he recommended that I look at the documentation from both him and
> Elaine...Anything you can recommend on this would be greatly
> appreciated...
>
> Sincerely,
> P. Therese Downing
> Kuntz Lab
>
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