Encountering some issues with reduce2 to add hydrogens to protein

[liyue9129]

Hi,
I encountered an issue when using reduce2 to add hydrogens to my protein. Some amino acids have an extra hydrogen atom added to their amide bonds, which caused problems in my subsequent protein preparation using meeko. I've attached my code below.
`
''

os.environ['MMTBX_CCP4_MONOMER_LIB'] = f"{my_path}/geostd"

os.system(f"python {my_path}/reduce2.py 7WKL_CAQ.pdb output.file_name=7WKL_CAQ_FH.pdb approach=add add_flip_movers=True")`

Could you please help me identify where I might be going wrong? Here are two examples(before and after hydrogenation) of where reduce2 has added an extra hydrogen atom.

7WKL_CAQ.zip

Axtra hydrogen atoms were added to the amide of 'A:109' and 'A:113'.

7TUO_KL9.zip
Axtra hydrogen atoms were added to the amide of 'A:321' and 'A:322'.

Thank you !

[nwmoriarty]

Can you be more specific? I looked at the locations in the files you mentioned and am unclear on the issue. You can cut out three residues and send just that to me with a more detailed explanation for what you see as wrong. Cheers Nigel

…

--- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : ***@***.*** Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

On Sun, Oct 27, 2024 at 7:21 PM liyue ***@***.***> wrote: Hi, I encountered an issue when using reduce2 to add hydrogens to my protein. Some amino acids have an extra hydrogen atom added to their amide bonds, which caused problems in my subsequent protein preparation using meeko. I've attached my code below. reduce_opts = "approach=add add_flip_movers=True" os.environ['MMTBX_CCP4_MONOMER_LIB'] = f"{my_path}/geostd" os.system(f"python {my_path}/reduce2.py 7WKL_CAQ.pdb output.file_name=7WKL_CAQ_FH.pdb {reduce_opts}") Could you please help me identify where I might be going wrong? Here are two examples(before and after hydrogenation) of where reduce2 has added an extra hydrogen atom. 7WKL_CAQ.zip <https://github.com/user-attachments/files/17536354/7WKL_CAQ.zip> Axtra hydrogen atoms were added to the amide of 'A:109' and 'A:113'. image.png (view on web) <https://github.com/user-attachments/assets/4ce78734-9d12-42f8-889e-265fe4d45af9> 7TUO_KL9.zip <https://github.com/user-attachments/files/17536390/7TUO_KL9.zip> Axtra hydrogen atoms were added to the amide of 'A:321' and 'A:322'. image.png (view on web) <https://github.com/user-attachments/assets/d92139cc-87db-4cf8-8b27-bf2b6ec739a4> Thank you ! — Reply to this email directly, view it on GitHub <#1026>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHYQPHT3QS6OSXJCVJBRQTZ5WNSJAVCNFSM6AAAAABQWNT4WGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGYYTOMJRGY3DIMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[liyue9129]

Thank you for your response！
I apologize for the confusion. Instead of adding extra hydrogens, the hydrogen added to one amino acid is too close to another amino acid.
I will cut out the two residues and send them along with a more detailed explanation of the issue I am encountering.

Example1：
As depicted in the red box, the hydrogen atom is participating in a covalent bond with both ASP113 and LYS109.
7WKL_CAQ_FH_cut.zip

Example2：
The hydrogen atom on the amino group of GLY322 is too close to the carbonyl oxygen of ASN321, as shown in the red box.
7TUO_KL9_FH_cut.zip

Thank you ！