Dear Amber Developersand Users,
I want to use MCPB.py to construct a nonbonded model (12-6 LJ Nonbonded Model) for a ligand-bound metalloprotein. Following the workflow described in the Amber 24 manual: “For the modeling of a non-bonded model with a refitted charge, users can follow the workflow (3 steps): 1m → 3b → 4n1.”
”””
MCPB input file (mcpb.in) is as follows:
original_pdb 6wfj_H.pdb
group_name 6wfj
ion_ids 12980 12981
ion_mol2files ZN1.mol2 ZN2.mol2
force_field ff14SB
water_model SPCE
gaff 1
large_opt 1
cut_off 2.8
lgmodel_chg 0
lgmodel_spin 1
”””
Step 1 (MCPB.py -i mcpb.in -s 1m) and Step 2 (MCPB.py -i mcpb.in -s 3b) successfully ran. However, when doing Step3 (MCPB.py -i mcpb.in -s4n1), the following error was encountered:
Traceback (most recent call last):
File "/share/apps/amber/cpu/21/bin/MCPB.py", line 712, in <module>
gene_leaprc(gname, orpdbf, fipdbf, stpdbf, stfpf, ionids, ionmol2fs,
File"/share/apps/amber/cpu/21/lib/python3.8/site-packages/pymsmt/mcpb/amber_modeling.py", line 201, in gene_leaprc
frcmodf = get_frcmod_fname(element, chg, watermodel, paraset)
File "/share/apps/amber/cpu/21/lib/python3.8/site-packages/pymsmt/mcpb/amber_modeling.py", line 108, in get_frcmod_fname
return frcmodf
UnboundLocalError: local variable 'frcmodf' referenced before assignment
I tried to change the water_model as TIP3P, but the error is already existed.Could anyone tell me why this error occurs?
Thank you very much for your time and assistance.
Best regards,
Weihao Zhang
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Received on Tue May 19 2026 - 01:00:03 PDT
