[AMBER] Mutation by pdb4amber

From: mohamed marzouk <mohamedmarzoukphysics.gmail.com>
Date: Fri, 15 Oct 2021 21:41:50 +0900

I am trying to mutate the protein R156Q using this command
 pdb4amber -i 1TSRB_wt.pdb -o 1TSRB_R248Q.pdb -m "156-GLN”
But I got message that Missing heavy atoms, so I checked the pub file I found the new Glutamine residue contains only 4 heavy atoms
Attached photo for them, while they should be 9 atoms.
I don’t know what is the reason ??

Anyway, I tried to do the mutation by Chimera and it had done, but Got another error during removing clashes that

No MMTK name for atom "N" in standard residue “NME”

Which means that there is a problem with the protein caping by AMBER.
Any suggestions ? To make mutation and remove clashes ?
I am trying now with Pymol !!!

Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.

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Received on Fri Oct 15 2021 - 06:00:03 PDT
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