Hi Marc, you're right- igb=8 is parameterized for proteins and peptides
only. We are working on nucleic acid parameters but they aren't done yet.
we did not have success with nucleic acids and igb=5, so I'm not sure how
well that would work in your case.
in general, when using implicit solvent for a system outside what has been
tested, people should proceed with extreme caution.
carlos
On Fri, Oct 5, 2012 at 6:10 AM, Marc van der Kamp
<marcvanderkamp.gmail.com>wrote:
> Dear all,
>
> This is mostly to warn others that may be as naive as I was ;)
>
> I tried to simulate a protein with FMN co-factor bound (using the Schneider
> & Suhnel parameters from http://www.pharmacy.manchester.ac.uk/bryce/amber
> ).
> First, I tried igb=8, as this is probably the most accurate implicit
> solvent model for proteins.
> It turned out that within 0.5ps (yes, picoseconds) heating from 10 to 50K,
> the phosphate moiety on FMN flew out of its binding pocket (with which
> there were several hydrogen bonds to the phosphate oxygens).
>
> This problem is not present when igb=5 (or 2) is used.
> So I presume the warning in the manual (for igb=7, so should also apply to
> igb=8) stating "This method is not recommended for systems involving
> nucleic acids", can be extended to "This method is not recommended for
> systems involving nucleic acids OR other phosphate-group containing
> systems".
>
> As I am relatively new to using implicit solvent, I'd like to ask:
> Is igb=5 the 'recommended' model for protein + phosphate-moiety containing
> cofactors?
>
> Thanks,
> Marc
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Received on Fri Oct 05 2012 - 05:00:02 PDT
