Dear, Mr. Swail,
Thank you for kind support.
I'll try capping terminal.
Yours sincerely,
Ikuo Kurisaki
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, February 06, 2012 3:17 AM
To: AMBER Mailing List
Subject: Re: [AMBER] GL4 at C-terminal
Hello,
There are no terminal titratable residues defined in the method. There are
some complications regarding backbone charge sets and their impact on
reference energies. While it is possible to define this residue, it's very
involved (you have to generate the charge set for it -- do you want the
terminus to titrate? If so, you need to generate effectively 25 charge
states corresponding with the 5 charge states for each carboxylate). Then
you need to calculate the reference energies (using TI with some
adjustments for entropic considerations resulting from more numerous
protonated states than deprotonated states), and lastly you need to titrate
that reference compound to validate it.
You'll also need to add the C-terminal GL4 to the CPin.pm or cpin_data.py,
and make sure that the topology file distinguishes, via the residue name,
in some way between internal GL4 and C-terminal GL4 so that the cpinutil
script can pick out which is which.
In the end, it would probably be easier to just assign a protonation state
to that particular residue, add an ACE cap, or a glycine or something that
you expect to have a small effect on your protein.
HTH,
Jason
On Sun, Feb 5, 2012 at 7:56 AM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber users and developers,
>
>
>
> I would like to ask a question about the setting of constant pH MD.
>
>
>
> In preparing topology files, I found that constph.lib does not contain
>
> N- and C-terminal positioned Residue type for GL4 and AS4 as is usual
> residues.
>
>
>
> Is there some prepfiles anywhere, or we need to built it?
>
>
>
> My interested protein has Glutamate in the C-terminal, unfortunately.
>
>
>
> Thank you for usual support and advices,
>
> Yours sincerely,
>
>
>
> Ikuo Kurisaki
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 05 2012 - 17:00:02 PST
