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

From: Song, Lin <>
Date: Fri, 13 Nov 2020 16:47:44 +0000


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.


On Nov 13, 2020, at 8:41 AM, 辛志宏 <<>> 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

AMBER mailing list<>;!!HXCxUKc!n4O8jxqkimJncOIL-cB7o3ktY6t9n4wxVtiVdUEuxU7nDiMt1HaWL8KBCoJbNtgMtaS7z6yG$

AMBER mailing list
Received on Fri Nov 13 2020 - 09:00:03 PST
Custom Search