Dear Carlos,
I pretty well familiar that pKa of Ser on the
surface of protein exposed in the bulk water solvent
has pKa around 15 as well as small molecular ethyl alcohol,
etc. The catalytic Ser in proteases in some cases when isolated from
water solvent may be ionized. To simulate the situation I need
that one specific Ser should be set up as ionized in MD simulation.
How to define that case in TLEAP?
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il
________________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, March 10, 2016 1:16 PM
To: AMBER Mailing List
Subject: Re: [AMBER] problem with ionized residues
There are parameters for protonated Asp and Glu, the names are Ash and
Glh. Check those in your pdb file.
There are not parameters for deprotonated Ser in ff14SB. I would expect
this side chain to have a very high pka, perhaps 13 or so.
CS
On Mar 10, 2016 5:30 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
wrote:
> Dear AMBER experts,
>
>
> I have amber14 and AmberTools15 on my computer.
>
> In preparing protein for MD simulations I use TLEAP procedure.
>
> There are parameters in ff14SB force field for different forms of HIS:
> HID, HIE, HIP,
>
> so TLEAP recognize and well differentiate them .
>
> Unfortunately, I faced the problem with other ionized protein residues
>
> like protonated neutral ASP and GLU side residues, or deprotonated
>
> side residue of anionic SER gamma O atom.
>
> It seems that the corresponding parameters for ionized side residues
> are absent in the ff14BB force field, so TLEAP reports about fatal error.
>
>
> I would appreciate if somebody can advise me how to work the problem
> around.
>
>
> Thank you,
>
> Michael
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<
> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
> >
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>
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Received on Thu Mar 10 2016 - 04:00:03 PST
