Re: [AMBER] How to correct the H atom direction in the HIE residue?

--
Gustavo Seabra
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Friday, November 13, 2020 1:47:23 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] How to correct the H atom direction in the HIE residue?
>  From the picture you sent, it looks like you want HIP.
that's what I thought at first, but then realized that there is no H on one
of the ring C atoms in the picture. So I think it's just confused about
which atom is which, and likely because of H atoms being in the wrong
positions or having wrong names in the original pdb file.
On Fri, Nov 13, 2020 at 1:43 PM Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> As others have said, you need to correct the protonation state before using
> LEaP.
>
> 1. Determine which protonation state you really want. For each
> possibility,  Amber has a specific residue name. From the picture you sent,
> it looks like you want HIP.
>
> 2. Change the residue name in all atoms for this residue in the PDB file.
>
> 3. Use 'pdb4amber' with the option to remove all hydrogens to create a new
> PDB file tonuse with LEaP. Pay attention to all the checks and warnings you
> get from pdb4amber.
>
> 4. Finally, use this last PDB file in LEaP. Your residue should be
> constructed correctly now.
>
> All the best,
> Gustavo.
>
> On Fri, Nov 13, 2020, 8:41 AM 辛志宏 <xzhfood.njau.edu.cn> wrote:
>
> > Dear all,
> > I parmetered and solvented the enzyme and saved the top and rst as well
> as
> > PDB file successfully by tleap, and then open the top an rst file by VMD,
> > it was found that
> >
> >
> > the direction of H Aatom in the reside 269 is not correct, but it is
> > correct when I open the PDB file in the VMD, I don't know what's reason
> for
> > the same enzyme in
> >
> >
> > different file style, how to correct the error from the top and rst file.
> >
> >
> > Any help for the solution will be much appreciation.
> >
> >
> > Attachment are the two pictures
> >
> >
> > Zhihong Xin,
> >
> >
> > College of Food Science and Technology
> >
> >
> > Nanjing Agricultural Univisity
> >
> >
> >
> >
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