AMBER Archive (2008)

Subject: RE: AMBER: Amber GB problems on PMEMD !!

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Sep 25 2008 - 10:23:44 CDT

Hi Samantha,

> I then ran 80 ns simulation on a small 20 amino-acid protein TRP cage (PDB
> id : 2jof.pdb) as a test case. This protein completely unfolds and folds
> again within this time-scale (80 ns). Experimentally this small peptide is
> supposed to fold in 4 micro-seconds or so (in explicit water).

A number of people have seen similar problems with IGB=7. Note larger
numbers are do not always mean better... I.e. as with the fact that newer
force fields are not always better newer GB models are not necessarily
better either. In a lot of cases it takes quite a while before people start
to understand the quirks of the various models.

I would start by trying to switch to IGB=5 instead of 7 and use the mbondi2
radii set. You should also set the cutoff to 9999.0 so that you don't employ
a cutoff without PME it can be dangerous to use a cutoff with GB so unless
you really can't afford it experimentally you should run without a cutoff.

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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