Delete hydrogens from that HIs residue. Change its name to HIE or HIP or
HID as you want and proceed to tleap step.
On Thursday, July 20, 2017, Thakur, Abhishek <axt651.miami.edu> wrote:
> It gets protonated and turn to HIP
>
> Sent using OWA for iPhone
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com <javascript:;>>
> Sent: Thursday, July 20, 2017 12:22:21 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] His getting protonated to HIP
>
> 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
> <javascript:;>> wrote:
>
> > I have tried that, but could not get desired results
> >
> > Sent using OWA for iPhone
> > ________________________________
> > From: Hai Nguyen <nhai.qn.gmail.com <javascript:;>>
> > 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
> <javascript:;>> wrote:
> >
> > > Because His is inmy active site. So charge is differing
> > >
> > > Sent using OWA for iPhone
> > > ________________________________
> > > From: Hai Nguyen <nhai.qn.gmail.com <javascript:;>>
> > > 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
> <javascript:;>>
> > 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org <javascript:;>
> > > >
> > >
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Received on Thu Jul 20 2017 - 20:30:02 PDT
