Hi Michael,
You may be able to find some parameters online, but they would not match
ff14SB and would need adjustment of atom types and so on. I can help with
that if you have something to modify. Otherwise you would need to build
your own, following the procedures in the supporting info of the ff14SB
paper. It should be fairly simple since it only had the single rotatable
bond. If you go that route, check back here if you run into specific
problems.
CS
On Mar 10, 2016 6:33 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Mar 10 2016 - 04:00:05 PST
