AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jul 28 2008 - 08:52:08 CDT

Alan,
you might also use ff99SB- most people doing comparisons these
days find it performs better than ff03 with respect to NMR, etc.
we've used it extensively for HIV PR. In addition to having
correct termini, the side chain dihedrals match the charges-
in ff03 I don't think this is the case (maybe Yong can clarify this).
carlos

On Mon, Jul 28, 2008 at 9:21 AM, Alan <alanwilter_at_gmail.com> wrote:
> 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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-- 
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