Hi Jonathan,
I think the general consensus is that TIP4P-Ew is, to date, the best bulk
non-polarizable rigid water model in common use (do I need more qualifiers
on that statement?).
Solvation is, as ever, another question. David Mobley (*et al.*) wrote a
paper several years ago comparing TIP3P and TIP4P-Ew solvation free
energies that was quite informative but far from conclusive (there was also
a fairly serious correction published a few years back concerning a bug in
TIP4P code, but the paper is still worth reading). We recently compared
both models in a QM/MM study calculating reaction barriers for small
phosphoryl transfer reactions and found no statistical difference. I'm not
aware of any studies specifically comparing the effects on binding
energies, but am also not a zealous follower of the literature on that
subject.
Hope that helps,
Brian
On Tue, Apr 16, 2013 at 1:57 PM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> Hi All,
>
> I'm running some basic peptide (~15 residues)- protein (~90 residues)
> binding simulations for a friend/colleague. I just want to make sure I'm
> dotting all my i's and crossing all the t's in case he tries to publish
> this down the line.
>
> Presently I have been using the TIP3P solvent model in combination with
> running MM-PBSA. Are we going to run into (should we be concerned) any
> issues (reviewers-artifacts-etc.)? Would it be safer/smarter to use TIP4P
> or TIP5P?
>
> Thanks,
> Jonathan
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Tue Apr 16 2013 - 12:30:04 PDT
