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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>
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Received on Fri Nov 13 2020 - 11:00:02 PST
