What does your HIS turn to? Does that make sense? Does it have hydrogen?
Hai
On Thu, Jul 20, 2017 at 7:06 PM Thakur, Abhishek <axt651.miami.edu> wrote:
> I have tried that, but could not get desired results
>
> Sent using OWA for iPhone
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Thursday, July 20, 2017 12:00:06 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] His getting protonated to HIP
>
> 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 - 16:30:03 PDT
