Dear Amberusers,
Im trying to parametrize Vanadate ion (VO4)3- using MCPB.py from AmberTools.
Im having trouble in the final modeling step, when generating the frcmod file.
In the folder containing the VO4.in file, running
MCPB.py -i VO4.in -s 2
produces the following error:
******************************************************************
* Welcome to use the MCPB.py program *
* Version 6.0 *
* Author: Pengfei Li *
* Merz Research Group *
* Michigan State University *
* AND *
* Hammes-Schiffer Research Group *
* Yale University *
******************************************************************
The input file you are using is : VO4.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [1]
The variable ion_info is : []
The variable ion_mol2files is : ['V.mol2']
The variable original_pdb is : VO4.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 : []
The variable gaff is : 1
The variable group_name is : VO4
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 : ['O1.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 : TIP3P
The variable xstru is : 0
******************************************************************
* *
*===================Generate the Initial frcmod file=============*
* *
******************************************************************
Atoms which has changed the atom types: [1, 2, 3, 4, 5]
1-V.1-V : V --> M1
2-O1.2-O1 : O1 --> Y1
3-O1.3-O1 : O1 --> Y2
4-O1.4-O1 : O1 --> Y3
5-O1.5-O1 : O1 --> Y4
Traceback (most recent call last):
File "/usr/local/Caskroom/miniconda/base/bin/MCPB.py", line 657, in <module>
gene_pre_frcmod_file(ionids, premol2fs, stpdbf, stfpf, smresf, prefcdf,
File "/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py", line 132, in gene_pre_frcmod_file
print('YES', atyp2 + massparms[atyp1], file=fmf)
KeyError: 'O1'
Seemingly O1 atom type is not found, however I don’t understand why.
I enclosed the files that are necessary to reproduce the error. Any insight on how to solve the issue will be greatly appreciated.
Thank you,
Federica
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Received on Wed Apr 07 2021 - 08:30:03 PDT
