Hi Eugene,
This is because your log file doesn’t contain the atomic coordinates, or MCPB.py can not recognize these information from the log file you obtained.
Did you use GAMESS-US to do the QM calculations? If so, which version did you use?
Kind regards,
Pengfei
> On Jun 29, 2017, at 1:15 AM, Eugene Cha <eugenekhcha.gmail.com> wrote:
>
> I'm getting this error during step 2 of MCPB.py. I've looked as much as I
> could through the archives and google, but I'm not sure what the issue.
>
>
> How do I fix this error?
>
>
> Thanks
>
>
>
> Eugene
>
>
> ******************************************************************
>
> * Welcome to use the MCPB.py program *
>
> * Version 3.0 *
>
> * Author: Pengfei Li *
>
> * Merz Research Group *
>
> * Michigan State University *
>
> * AND *
>
> * Hammes-Schiffer Research Group *
>
> * University of Illinois at Urbana-Champaign *
>
> ******************************************************************
>
> The input file you are using is : NNQQNY_Cu.in
>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> The following is the input variable you have:
>
> The variable ion_ids is : [101]
>
> The variable ion_info is : []
>
> The variable ion_mol2files is : ['CU.mol2']
>
> The variable original_pdb is : NNQQNY_Cu_FINAL2_2.pdb
>
> The variable add_bonded_pairs is : []
>
> The variable add_redcrd is : 0
>
> The variable additional_resids is : []
>
> The variable anglefc_avg is : 0
>
> The variable bondfc_avg is : 0
>
> The variable chgfix_resids is : []
>
> The variable cut_off is : 2.8
>
> The variable force_field is : ff14SB
>
> The variable frcmod_files is : ['NNQ.frcmod']
>
> The variable gaff is : 1
>
> The variable group_name is : NNQQNY_Cu
>
> The variable ion_paraset is : CM (Only for nonbonded model)
>
> The variable large_opt is : 1
>
> The variable lgmodel_chg is : -99
>
> The variable lgmodel_spin is : -99
>
> -99 means program will assign a charge automatically.
>
> The variable naa_mol2files is : ['NNQ.mol2']
>
> The variable scale_factor is : 1.0
>
> ATTENTION: This is the scale factor of frequency. The
>
> force constants will be scaled by multiplying the square
>
> of scale_factor.
>
> The variable smmodel_chg is : -99
>
> The variable smmodel_spin is : -99
>
> -99 means program will assign a charge automatically.
>
> The variable software_version is : gms
>
> The variable sqm_opt is : 0
>
> The variable water_model is : TIP3P
>
> The variable xstru is : 0
>
> ******************************************************************
>
> * *
>
> *===================Generate the Initial frcmod file=============*
>
> * *
>
> ******************************************************************
>
> Atoms which has changed the atom types: [1, 7, 19, 22, 33, 101]
>
> 1-ASN.1-N : N --> Y1
>
> 1-ASN.7-O : O --> Y2
>
> 2-ASN.19-O : O --> Y3
>
> 2-ASN.22-O : O --> Y4
>
> 3-GLN.33-O : O --> Y5
>
> 7-CU.101-CU : CU --> M1
>
> ==================Using the Seminario method to solve the problem.
>
> Traceback (most recent call last):
>
> File "/Users/eugenecha/anaconda3/bin/MCPB.py", line 662, in <module>
>
> fcfchkf, fclogf, g0x, scalef, bondfc_avg, anglefc_avg)
>
> File
> "/Users/eugenecha/anaconda3/lib/python3.6/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py",
> line 731, in gene_by_QM_fitting_sem
>
> crds = get_crds_from_gms(logfile)
>
> File
> "/Users/eugenecha/anaconda3/lib/python3.6/site-packages/pymsmt/mol/gmsio.py",
> line 107, in get_crds_from_gms
>
> if bln is None:
>
> UnboundLocalError: local variable 'bln' referenced before assignment
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Received on Fri Jun 30 2017 - 14:30:04 PDT
