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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Received on Thu Mar 10 2016 - 03:30:09 PST
