Hi Zahra,
Could you kindly provide the MCPB.py input files? I did not see them in the Google Drive folder. It has a total of 50 files, but it appears that the most important input file (the one that contains original_pdb, group_name, etc.) is missing.
Additionally, without the small_opt.com, small_fc.com, and large_mk.com files, it is challenging to visualize and diagnose the issue that occurred while MCPB.py selects the region for QM calculation.
Based on the current clues, I can tell that TRP21 is -NH2, not NME-capped in the complex_mcpbpy.pdb. And tleap is doing something wrong by introducing this line "bond mol.21.C mol.42.N" (E42 is so far away, bonding them makes no sense).
However, again, without the MCPB input file, I cannot draw a conclusion why MCPB.py generates such a strange tleap input file. Thank you for any follow-up on this.
Best regards,
Zhen.
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org>,
Michigan State University,
Cleveland Clinic.
________________________________
From: Aliakbartehrani Zahra via AMBER <amber.ambermd.org>
Sent: Wednesday, May 21, 2025 3:41 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] missing angle/dihedral parameters issue after MCPB.py/tleap
Hi all,
I’ve recently started working with MCPB.py to parameterize a zinc-containing protein system. The MCPB.py workflow (using Amber18: model building, charge fitting, and parameter generation) was completed successfully. However, I'm encountering an issue at the tleap step: the program fails due to missing angle and dihedral parameters, including custom atom types like Y1 and Y2, involving residues Trp21, Gly22, and Glu42—note: Glu42 was not selected in the small/standard/large model for MCPB:
Could not find angle parameter for atom types: Y2 - C – N
Could not find angle parameter for atom types: C - N – C
Could not find angle parameter for atom types: Y3 - C – N
No torsion terms for atom types: N - C - Y2 - M1
These missing parameters appear to be linked to TRP21, an N-terminal tryptophan residue in my system that directly coordinates the Zn ion. MCPB.py generated this residue as TP1.mol2, and I would like to keep it in the –NH₂ terminal form, rather than converting it to the standard NTRP form. It seems the issue may stem from the following model-building step as creating 21-TRP into GLY and 22-GLY into NME, where MCPB.py replaces residues during model selection:
***Creating the small model...
Creating the residue 21-TRP into GLY...
Creating the residue 22-GLY into NME…
It contains the residue 65-ASP as sidechain coordinated.
It contains the residue 68-LYS as sidechain coordinated.
It contains the residue 80-HIE as sidechain coordinated.
It contains the residue 135-HID as sidechain coordinated.
It contains the residue 139-ASP as sidechain coordinated.
It contains the residue 145-HID as sidechain coordinated.
It contains the residue 168-HID as sidechain coordinated.
It contains the residue 172-ASP as sidechain coordinated.
It contains the residue 401-ZN as normal.
It contains the residue 402-ZN as normal.
It contains the residue 403-ZN as normal.
And some X-ray waters in coordination with Zincs
I’ve shared the relevant tleap and MCPB.py files for your review from the link below (tleap.in<
https://urldefense.com/v3/__http://tleap.in/__;!!HXCxUKc!wJ2M_53sKRHv1IwraDYXMUyDtarNj0xOYZqWRBSChPJ0zdrvjUyFYIj9XfCYbBtfCx0Yat3sdhdLGRy6GMZ8FEo$ >, leap.log, complex_mcpbpy.pdb, and complex_mcpbpy.frcmod).
https://urldefense.com/v3/__https://drive.google.com/file/d/1Z5C7_xfIIt6GrSVW4aac1mvsOeW08TjW/view?usp=sharing__;!!HXCxUKc!wJ2M_53sKRHv1IwraDYXMUyDtarNj0xOYZqWRBSChPJ0zdrvjUyFYIj9XfCYbBtfCx0Yat3sdhdLGRy60tYCuQ0$
I would be very grateful for any suggestions you might have on resolving this.
Bests
Zahra
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Received on Mon May 26 2025 - 21:30:02 PDT
