AMBER Archive (2008)

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

From: Alan (alanwilter_at_gmail.com)
Date: Mon Jul 28 2008 - 08:21:35 CDT

Yes, I see your point.

In this case it's a HIV Protease and the NPRO is not involved in the
active site, although it's not a flexible tail either. Anyway, even if
it was involved in active site, I never heard about building block
designed to have not integral charges. I checked all N- and C- termini
for ff03.r1 and only NPRO shows this oddity.

I am sticking with original ff03 for the moment.

Cheers,
Alan

On Mon, Jul 28, 2008 at 1:54 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> perhaps- but it is always good to think carefully about this
> before building your system. for example, one of our systems
> has the NPRO in the active site and it is intimately involved
> in substrate binding. terminal residues are not always just flexible tails.
> carlos
>
> On Mon, Jul 28, 2008 at 8:28 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
>> 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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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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