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 - 09:50:00 CDT

Thanks Carlos!

I will check ff99SB and papers.

Cheers,
Alan

On Mon, Jul 28, 2008 at 2:52 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> 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
>>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>> to majordomo_at_scripps.edu
>>>
>>
>>
>>
>> --
>> 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<<
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
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<<
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu