yes, if you want them protonated, those are the names to use. they are not
available in all force fields, so you'll need to look carefully at the
files and at the Leap output.
On Mon, Aug 6, 2012 at 9:39 PM, Zalikha Ibrahim
<zalikha.ibrahim.yahoo.com>wrote:
> Thanks so much f quick reply.
> How about aspartate and glutamate that have high pKa at pH 7? And
> basically when the ASH and GLH naming being applied?
> I should let you know that I previously sent the protein to a web-based
> software for pKa prediction.
>
> Zalikha
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>; Zalikha Ibrahim <
> zalikha.ibrahim.yahoo.com>
> Sent: Tuesday, August 7, 2012 9:23 AM
> Subject: Re: [AMBER] Aspartate and Glutamate naming in PDB
>
> A low pka would mean they are deprotonated at ph 7, so don't change them.
> On Aug 6, 2012 9:21 PM, "Zalikha Ibrahim" <zalikha.ibrahim.yahoo.com>
> wrote:
>
> > Hi to all Amber user,
> >
> > I have a question about the naming of aspartate and glutamate in PDB.
> > Please correct me if I wrong.
> > Aspartate and Glutamate are recognized in their deprotonated form by
> > default in XLeap (ASP and GLU). If I want to simulate the protein in pH
> 7,
> > should I change the name of all aspartate and glutamate residues that has
> > low pKa value at pH 7 as ASH and GLH?
> >
> > Thanks so much in advance
> >
> > Zalikha Ibrahim
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Aug 07 2012 - 05:00:02 PDT
