[AMBER] phosphate moiety & igb model

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Fri, 5 Oct 2012 11:10:21 +0100

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

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

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Received on Fri Oct 05 2012 - 03:30:03 PDT
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