[AMBER] KeyError of chargedict in MCPB's step 1

From: Ge Song via AMBER <amber.ambermd.org>
Date: Thu, 4 Sep 2025 15:47:45 +0000

Dear Amber developers,

I have got the same error in running MCPB step 1 as posted here before (http://archive.ambermd.org/202006/0052.html):

  File "/home/software/AMBER/19/amber18/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1690, in gene_model_files
    totchg = totchg + chargedict['C' + mol.residues[i].resname]
KeyError: 'CSAM'

According to the previous reply from pengfei (http://archive.ambermd.org/202006/0100.html), matching the atom names in mol2 file with original_pdb file should solve the problem, but this is not the case for me.


I did include the SAM.mol2 file:

original_pdb 1TV8_cym.pdb
group_name fs_clusters
ion_ids 5308 5309 5310 5311 5316 5317 5318 5319
ion_mol2files FE2.mol2 FE2.mol2 FE2.mol2 FE3.mol2 FE2.mol2 FE2.mol2 FE2.mol2 FE2.mol2
naa_mol2files SF4.mol2 SAM.mol2 SO4.mol2
force_field ff14SB
water_model tip3p
cut_off 2.8
charge_method resp
qm_theory B3LYP
basis_set 6-31G*

And the atom names exactly match with the original pdb.

I am wondering if anyone could give me some suggestions (I have attached the 1TV8_cym.pdb abd all mol2 files I am using).

Best,
Ge
[https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]1TV8_cym.pdb<https://prodduke-my.sharepoint.com/:u:/g/personal/gs298_duke_edu/EY-yYHosL01PtggK1cHP1DEBciKErRX0io073Hs5dtVvRw>
[https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]FE2.mol2<https://prodduke-my.sharepoint.com/:u:/g/personal/gs298_duke_edu/EZEKOVjfMplAsp9RJsR71OoB8ffpHpd9qoZ5je2TcMY5pQ>
[https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]FE3.mol2<https://prodduke-my.sharepoint.com/:u:/g/personal/gs298_duke_edu/EevdAaEWv1JComYBrqRcFpsB5PQ4XwLSJArNmO-6EGN1Sw>
[https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]SAM.mol2<https://prodduke-my.sharepoint.com/:u:/g/personal/gs298_duke_edu/ESH1S34rxL9OgoJPUfAvWoQBUzPYkYQ1tokE3qruujDvfA>
[https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]SO4.mol2<https://prodduke-my.sharepoint.com/:u:/g/personal/gs298_duke_edu/EYVxx8w2LOxBk7n1HLvxObsBaBMVsBU5KQhRQQdi_zeE4w>

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Received on Thu Sep 04 2025 - 09:00:03 PDT