AMBER Archive (2009)

Subject: RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Dec 04 2009 - 13:16:50 CST

> > My question came because I have done some MD with the CHARMM (Klauda
> et al.)
> > and GLYCAM06 ff and I would like to explain in my paper why I found
> some a
> > slight difference (~12%, GLYCAM06=84% and CHARMM=72%) in the average
> trans
> > population for the CCCC angles in the alkyl chain between these two
> ff.
> > Since these results are similar that others ones obtained in my lab
> with the
> > FF99SB parameters, I am not worried about this result.
>
> May-be the differences underlined by Ross are responsible of these 12
> % differences...

I should add to this that GLYCAM06 was parameterized to not use 1-4 scaling
of electrostatics and VDW. Hence if you are using Glycam then you should set
SCNB=1.0 and SCEE=1.0 in the cntrl namelist. But do this ONLY if you are
using Glycam. For FF99SB, FF03 etc this should be left at the defaults of
SCNB=2.0 and SCEE=1.2. Currently if you mix Glycam and FF99SB in a single
simulation then you have to choose one setting or the other. AMBER 11 will
include a solution to this to allow you to mix things correctly.

Hence if you ran your Glycam simulations without correctly setting this then
that could also account for some of the difference.

All the best
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 | http://www.wmd-lab.org/ |

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