Dear Amber users
I am trying to parameterize iron for my system but could not solve the
following problem. I have checked for a solution on the amber community but
could not figure it out as the only suggestion mention was checking the
metal id. I have checked it and could not see any problem associated with
input files. I have attached the input file for your reference.
[surendra.gpu MCPB]$ MCPB.py -i 5L9B.in -s 1
******************************************************************
* Welcome to use the MCPB.py program *
* Version 4.0 *
* Author: Pengfei Li *
* Merz Research Group *
* Michigan State University *
* AND *
* Hammes-Schiffer Research Group *
* UIUC and Yale *
******************************************************************
The input file you are using is : 5L9B.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [4018]
The variable ion_info is : []
The variable ion_mol2files is : ['FE.mol2']
The variable original_pdb is : 5l9b_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 : ff14SB
The variable frcmod_files is : ['AKG.frcmod']
The variable gaff is : 1
The variable group_name is : 5L9B
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 : ['WAT.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 : g03
The variable sqm_opt is : 0
The variable water_model is : TIP3P
The variable xstru is : 0
Traceback (most recent call last):
File "/home/surendra/anaconda2/bin/MCPB.py", line 577, in <module>
addbpairs)
File
"/home/surendra/anaconda2/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
line 51, in get_ms_resnames
resid = mol.atoms[i].resid
KeyError: 4018
Thank you
Best Regards
Mahesh
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- application/octet-stream attachment: 5L9B.in
- application/octet-stream attachment: AKG.mol2
- application/octet-stream attachment: WAT.mol2
- application/octet-stream attachment: FE.mol2
Received on Tue Apr 02 2019 - 22:30:02 PDT
