Re: [AMBER] His getting protonated to HIP

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Thu, 20 Jul 2017 22:13:00 -0500

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
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> > > >
> > >
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Received on Thu Jul 20 2017 - 20:30:02 PDT
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