What I do is I rename the residue in the pdb file. The default of leap is
to use the epsilon-His, or HIE. Based on the pictures you attached, it
seems what you want is the protonated His. Just rename the residue to HIP
in the text file, and re-run your leap script. If you want the delta-His,
then use HID.
On Sat, Nov 14, 2020 at 12:51 AM Song, Lin <songlin3.chemistry.msu.edu>
wrote:
> Hi,
>
> First, HE is Histidine with hydrogen on the epsilon nitrogen, not on both
> hydrogen, so your PDB file in VMD does not look fine.
>
> Second, for the connectivity problem, PDB will display bonds between atoms
> based on distance, so if the distance between two atoms are small, it will
> assign bond between them. For the rst and prmtop file, it will show the
> connectivity generated by leap. I think the problem here is the atom names
> in the original PDB is messed up. You can try changing the CD2 to ND1, ND1
> to CD2, NE2 to CE1, CE1 to NE2, HE2 to HE1, HE1 to HE2 in the original PDB
> and use leap to generate the topologies again. Or you can delete the
> hydrongens and let leap add them.
>
> Best,
> Lin
>
> On Nov 13, 2020, at 8:41 AM, 辛志宏 <xzhfood.njau.edu.cn<mailto:
> 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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Received on Fri Nov 13 2020 - 11:00:02 PST
