using the PDB file shows you bonds based on distance. using the parm file
in VMD shows you bonds actually in Amber. that is the one you should look
at to understand what you are simulating.
It seems unlikely that leap would have put the H atom in the wrong
location. Is it possible that your loaded a pdb file into leap that already
included H atoms? If so, it could be an atom naming problem and it may be
best to remove the H atoms and let leap build them.
On Fri, Nov 13, 2020 at 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 - 06:00:05 PST
