Hi,
We'll post a bugfix for this; in the mean time try this patch:
Insert a new line to assign bln the default value None in file gmsio.py, eg:
.. -90,6 +90,7 .. def get_crds_from_gms(logfile):
unit = 'angs' #Coordinates will use angs unit in default
+ bln = None
ln = 1
fp = open(logfile, 'r')
for line in fp:
Thanks for the report,
scott
On Thu, Jun 29, 2017 at 03:15:55PM +0900, Eugene Cha 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.
> ******************************************************************
> * 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 Thu Jun 29 2017 - 12:30:04 PDT
