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<
http://tleap.in/>, leap.log, complex_mcpbpy.pdb, and complex_mcpbpy.frcmod).
https://drive.google.com/file/d/1Z5C7_xfIIt6GrSVW4aac1mvsOeW08TjW/view?usp=sharing
I would be very grateful for any suggestions you might have on resolving this.
Bests
Zahra
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Received on Wed May 21 2025 - 01:00:03 PDT
