Re: [apbs-users] question about interaction energies. .

[Martin, E. W <Erik.Martin@STJUDE.ORG>]

Thanks for the replies.  I might not have been clear enough with my
question.  Obviously, there are other components to binding other than the
electrostatics.  However, the result of this calculation still seemed
counter intuitive given the nature of the charges on the peptide ligand
and the binding surface.  I was assuming that there must be some
unfavorable interactions I'm not intuitively visualizing.

I was wondering if there was a straight forward way in apbs to look at the
specific interaction energies at individual atoms, residues or even grid
points to attempt to determine which part of the peptide is
electrostatically favorable or unfavorably with the protein surface.

Thanks a lot,
Erik

On 11/30/12 12:45 PM, "Baker, Nathan" <Nat...@pn...> wrote:

>Yes, this is a good point:  my response was focused on the polar part of
>the solvation energy.
>
>Thanks,
>
>--
>Nathan Baker
>Pacific Northwest National Laboratory
>Phone:  +1-509-375-3997
>http://nabaker.me
>
>From: Aron Broom <bro...@gm...<mailto:bro...@gm...>>
>Date: Friday, November 30, 2012 12:51 PM
>To: Nathan Baker <nat...@pn...<mailto:nat...@pn...>>
>Cc: Erik Martin <Erik.Martin@STJUDE.ORG<mailto:Erik.Martin@STJUDE.ORG>>,
>APBS-USERS mailing list
><apb...@li...<mailto:apb...@li...>
>>
>Subject: Re: [apbs-users] question about interaction energies
>
>Also, what about VDW forces?  I'm not confident about the idea that the
>binding would involve "no" conformational change, but for sure it would
>involve VDW changes.
>
>Additionally, did you include a quasi-harmonic approximation for the
>entropy?  Maybe the binding is actually entropically favourable (I
>believe that is somewhat rare, but not unheard of).
>
>~Aron
>
>On Fri, Nov 30, 2012 at 11:26 AM, Baker, Nathan
><Nat...@pn...<mailto:Nat...@pn...>> wrote:
>Hello --
>
>The desolvation of the protein is generally an unfavorable energetic
>contribution that can offset favorable Coulombic interactions.  This
>unfavorable effect increases as the protein dielectric decreases.
>
>Thanks,
>
>--
>Nathan Baker
>Pacific Northwest National Laboratory
>Phone:  +1-509-375-3997<tel:%2B1-509-375-3997>
>http://nabaker.me
>
>
>
>
>
>On 11/29/12 11:18 AM, "Martin, Erik W"
><Erik.Martin@STJUDE.ORG<mailto:Erik.Martin@STJUDE.ORG>> wrote:
>
>>
>>I recently did a quick calculation following the binding energy example
>>(and recent thread on this list).  Essentially all I did was subtract the
>>protein alone and peptide alone from the complex.  What confused me is
>>that this interaction "should" be purely electrostatic and involve no
>>conformational change.   The result I got was a net positive energy
>>(albeit relatively low ~3kJ/mol).  This confused me, by inspection, there
>>is no reason this interaction should be repulsive (even if weakly).
>>
>>I can only imagine that there is some significantly repulsive interaction
>>I'm not noticing.  Is there someway for me to get the per residue
>>interaction energies?  That is to say, have apbs output the energy per
>>residue or atom without redoing this type of calculation and individually
>>removing amino acids from the peptideŠ
>>
>>Thanks a lot,
>>Erik
>>
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>--
>Aron Broom M.Sc
>PhD Student
>Department of Chemistry
>University of Waterloo
>
>