Hi Gustavo,
Can you send me the sample files? I will check the error.
Best,
Pengfei
> On Oct 17, 2022, at 11:11 AM, Gustavo Seabra via AMBER-Developers <amber-developers.ambermd.org> wrote:
>
> Hi everyone,
>
> I'm sorry if you got this message duplicated. I have sent it last week to
> the users' list, but it got no answers, so I assume it passed unnoticed
> there.
>
> I'm trying to build a system with an Fe2+ center, and using OPC water. The
> manual states that, in AmberTools 22, MCPB.py should be compatible with OPC
> water.
>
> However, when trying to build the system with OPC water, I get
> the following message:
> <--
> $ MCPB.py -i MCPB.in -s 1
> [...]
> Totally there are 105 atoms in the large model.
> Totally there are 450 electrons in the large model.
> Traceback (most recent call last):
> File "/opt/miniconda3/envs/AmberTools22/bin/MCPB.py", line 651, in
> <module>
> gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
> File
> "/opt/amber/current/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1909, in gene_model_files
> build_large_model(mol, reslist, lmsresids, lmsresace, lmsresnme,
> lmsresgly,
> File
> "/opt/amber/current/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1600, in build_large_model
> IonLJParaDict = get_ionljparadict(watermodel)
> File
> "/opt/amber/current/lib/python3.7/site-packages/pymsmt/mol/element.py",
> line 325, in get_ionljparadict
> IonLJParaDict.update(diljpara2)
> UnboundLocalError: local variable 'diljpara2' referenced before assignment
> -->
>
> If I just replace the OPC model by TIP3P in the water_model line, it works
> just fine.
>
> Was anyone else successful in building the model with OPC waters? (If
> anyone wants, I can send sample files to reproduce the error).
>
> Thanks,
> --
> Gustavo Seabra.
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Received on Tue Oct 18 2022 - 15:00:02 PDT
