HI Eric,
This pdb file should be generated when you run the first step of MCPB.py modeling, it contain the metal site information only, which is needed for the next steps.
Hope it helps,
Pengfei
> On Mar 27, 2025, at 1:50 PM, Hantz, Eric via AMBER <amber.ambermd.org> wrote:
>
> 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 - 14:00:02 PDT
