Hello,
I'm trying to using MCPB.py to parameterize the metal binding site for a zinc binding protein. I am following the instructions in:
Advanced Tutorial 20 -
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php
Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program -
https://pubmed.ncbi.nlm.nih.gov/33125655/
I've run the DFT calculations for the small and large subsystems:
$ g16 <{system}_coord_small_opt.com > {system}_coord_small_opt.log
$ g16 <{system}_coord_small_fc.com > {system}_coord_small_fc.log
$ formchk {system}_coord_small_opt.chk {system}_coord_small_opt.fchk
$ g16 <{system}_coord_large_mk.com > {system}_coord_large_mk.log
I run into problems when performing the remaining steps of the MCPB protocol:
$ MCPB.py -i mcpb_input.in -s 2
>******************************************************************
>* *
>*===================Generate the Initial frcmod file=============*
>* *
>******************************************************************
>Traceback (most recent call last):
> File "/home/ucsf/miniforge3/envs/AmberTools23/bin/MCPB.py", line 665, in <module>
> gene_pre_frcmod_file(ionids, premol2fs, stpdbf, stfpf, smresf, prefcdf,
> File "/home/ucsf/miniforge3/envs/AmberTools23/lib/python3.12/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py", line 70, in
> gene_pre_frcmod_file
> mol, atids, resids = get_atominfo_fpdb(stpdbf)
> ^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/ucsf/miniforge3/envs/AmberTools23/lib/python3.12/site-packages/pymsmt/mol/pdbio.py", line 19, in get_atominfo_fpdb
> fp = open(fname, 'r')
> ^^^^^^^^^^^^^^^^
> FileNotFoundError: [Errno 2] No such file or directory: '{system}_coord_standard.pdb'
I haven't seen anything in the manual or tutorials about creating "{system}_coord_standard.pdb" this is different from the original pdb flag in the mcpb_input.in file. What should this file contain?
Best,
Eric
_______________________________________
Eric Hantz
Postdoctoral Research Fellow - Renslo Lab
UCSF - Pharmaceutical Chemistry
Email: eric.hantz.ucsf.edu
Phone: 570-688-8720
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Received on Thu Mar 27 2025 - 12:00:02 PDT
