If your original pdb have hydrogen, you can give pdb4amber (ambertools 17)
a shot
pdb4amber your.pdb
Ps: not 100% sure if works.
Hai
On Thu, Jul 20, 2017 at 6:52 PM Thakur, Abhishek <axt651.miami.edu> wrote:
> Because His is inmy active site. So charge is differing
>
> Sent using OWA for iPhone
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Thursday, July 20, 2017 11:32:49 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] His getting protonated to HIP
>
> Why do you need to do that?
> Hai
>
> On Thu, Jul 20, 2017 at 6:27 PM Thakur, Abhishek <axt651.miami.edu> wrote:
>
> > Hi,
> >
> > I am trying to make a complex file of my system and ligand,
> unfortunately,
> > all my HIS is getting protonated and getting converted to either HIE or
> HIP.
> >
> >
> > I was wondering is there any way to prevent this? or I can delete
> > hydrogens from HIP to make it HIS in my prmtop and inpcrd file?
> >
> >
> >
> > Thanking you,
> >
> > -Abhishek
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> >
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Received on Thu Jul 20 2017 - 16:30:02 PDT
