AMBER Archive (2008)

Subject: Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why?

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Jul 28 2008 - 07:28:50 CDT

Quoting Alan <alanwilter_at_gmail.com>:

> Is nobody concerned about the fact that in
> amber10/dat/leap/lib/all_aminont03.lib and
> amber10/dat/leap/prep/all_aminont03.in NPRO has net charge 0.900026
> and not 1.000?

I did not check. It seems this is not normal.

> I've read Duan 2003 and searched here in the list. I am sorry but if
> it's not error, so what would be? Besides, Amber Tools manuals even
> recommend leaprc.ff03.r1, but it's impossible to use it with a system
> with NPRO.

A temporary alternative would be to use the Duan et al. FF as it was
implemented in Amber8/9, i.e. using the terminal fragments from the
Cornell et al FF in the Duan et al FF. The terminal fragments of a
protein are exposed to the solvent; so using those form the Cornell et
al FF should be ok.

regards, Francois

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