Hi users,
I want to create an itp file for my ligand (ligand with ruthenium)
complex, im using MCPB.Py for generating itp for my structure during the
process i got the following error kindly please help.
MCPB.py -i dna.in -s 3
******************************************************************
* Welcome to use the MCPB.py program *
* Version 7.0 *
* Author: Pengfei Li *
* Merz Research Group *
* Michigan State University *
* AND *
* Hammes-Schiffer Research Group *
* Yale University *
* AND *
* Li Research Group *
* Loyola University Chicago *
******************************************************************
The input file you are using is : dna.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [1201]
The variable ion_info is : []
The variable ion_mol2files is : ['Ru.mol2']
The variable original_pdb is : complex_fixed_h.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 : ff19SB
The variable frcmod_files is : ['LIG.frcmod']
The variable gaff is : 1
The variable group_name is : dna
The variable ion_paraset is : 12_6 (Only for the ions using the
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 : ['LIG.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 : gau
The variable sqm_opt is : 0
The variable water_model is : OPC
The variable xstru is : 0
******************************************************************
* *
*======================RESP Charge fitting=======================*
* *
******************************************************************
***Generating the 1st stage resp charge fitting input file...
***Generating the 2nd stage resp charge fitting input file...
***Doing the RESP charge fiting...
=========================Checking models==========================
***Check the large model...
Good. The charges and atom numbers are match for the large model.
Good. There are 27 atoms in the large model.
***Check the standard model...
Traceback (most recent call last):
File "/home/saranya/amber20/bin/MCPB.py", line 692, in <module>
resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids,
ff_choice,
File
"/home/saranya/amber20/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py",
line 521, in resp_fitting
raise pymsmtError('Error: the charges and atom numbers are mismatch
'
pymsmt.exp.pymsmtError: Error: the charges and atom numbers are mismatch
for the standard model!
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Received on Tue Nov 22 2022 - 07:30:03 PST
