Dear Amber Community, following the tutorial for MCPB.py
<
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php>. I tried to
parametrise the Zinc ion using MCPB following the same naming convention
used in the tutorial.
I was able to run Gaussian and perform the Merz-Kollman RESP charge
calculation for the large model. My system of interest is human carbonic
anhydrase II (PDB ID: 3d92). However, post the gaussian calculation, I got
the following error when I try to run this command :
MCPB.py -i 3d92.in -s 2
The error :
"*===================Generate the Initial frcmod file=============*
* *
******************************************************************
Atoms which has changed the atom types: [1417, 1454, 1797, 4058, 4059]
91-HID.1417-NE2 : NB --> Y1
93-HID.1454-NE2 : NB --> Y2
116-HIE.1797-ND1 : NB --> Y3
258-ZN.4058-ZN : ZN --> M1
259-MOH.4059-O : oh --> Y4
==================Using the Seminario method to solve the problem.
Traceback (most recent call last):
File "/home/cclab/miniconda3/envs/AmberTools23/bin/MCPB.py", line 670, in
<module>
gene_by_QM_fitting_sem(smpdbf, ionids, xstru, stfpf, prefcdf, finfcdf,
File
"/home/cclab/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py",
line 729, in gene_by_QM_fitting_sem
crds = get_crds_from_fchk(chkfname, len(atids))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/cclab/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/pymsmt/mol/gauio.py",
line 369, in get_crds_from_fchk
for line in fp:
File "<frozen codecs>", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0:
invalid start byte"
Could someone help me figure out where I am going wrong. Kindly find the
attached zipped folder.
Additionally, I have tried to use ZAFF for the parameterization of Zinc.
Following the ZAFF tutorial for parameterizing, however, I encountered an
issue during the production run using pmemd, where the simulation
terminated with the following error:
> "Hydrogen atom 4101 appears to have multiple bonds to atoms 4102 and
4101, which is illegal for SHAKEH.
> Exiting due to the presence of inconsistent SHAKEH hydrogen clusters."
I believe this issue might be related to the warnings/notes I received
after the tleap process:
> "1-4: angle 4101 4102 duplicates bond ('triangular' bond) or angle
('square' bond)
> 1-4: angle 4101 4103 duplicates bond ('triangular' bond) or angle
('square' bond)
> 1-4: angle 4102 4103 duplicates bond ('triangular' bond) or angle
('square' bond)"
I suspect that my water molecule may not be properly coordinating with the
Zinc ion, which could be contributing to this issue. I would appreciate any
insights on whether this could be a possible cause and how to ensure
correct coordination.
To provide more context, kindly find attached the following files, the
tleap input file, the log file and the input PDB used in the study.
I would appreciate any insights or suggestions on how to resolve this
issue. Thank you for your time and guidance.
MCPB.py.zip
<
https://drive.google.com/file/d/1GKOSz2pk7Baq2Ph31ZLAgozHEZJEKg0c/view?usp=drive_web>
Thanks and regards
Dipankar
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Received on Tue Mar 25 2025 - 08:00:03 PDT
