Yes, there was a problem with ZN.mol2. Now I can solve the problem.
Thank you
________________________________
From: Pengfei Li <ambermailpengfei.gmail.com>
Sent: Wednesday, January 31, 2018 4:36:12 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MCPB.py error with ion id
Hi Abhishek,
Is your ZN.mol2 OK?
Pengfei
> On Jan 29, 2018, at 9:37 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
> I everyone I am getting the following error. when I am trying to generate the frcmod file
> MCPB.py -i YYY.in -s 2
>
> Atoms which has changed the atom types: []
> Traceback (most recent call last):
> File "/nethome/axt651/apps/amber16_tools/bin/MCPB.py", line 657, in <module>
> ff_choice, gaff, frcmodfs, watermodel)
> File "/nethome/axt651/apps/amber16_tools/lib/python2.7/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py", line 121, in gene_pre_frcmod_file
> attyp = attypdict[i][1]
> KeyError: 11026
>
> where atom 11026 seems is my metal id
>
> HETATM11026 ZN ZN 696 6.014 3.972 7.294 1.00 0.00 ZN
>
>
>
> ##my input file
>
> original_pdb YYY_H_renum.pdb
> group_name YYY
> cut_off 2.8
> ion_ids 11026
> software_version g09
> ion_mol2files ZN.mol2
> naa_mol2files MOL.mol2 HOH.mol2
> frcmod_files MOL.frcmod HOH.frcmod
>
> I have crossed checked the atom number and don't know what should be next logical step.
> Kindly help me.
>
>
> Thanking you,
> -Abhishek
>
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Received on Wed Jan 31 2018 - 09:00:03 PST
