Hello Amber users,
I am modeling a metal ligand complex (ion-pair) for which I need to run a MD. I am using the MCPB.py script to generate the final prmtop and inpcrd files. I ran the Gaussian calculations on the small and large models generated but while performing step 3 of modeling, I am getting an error:
he input file you are using is : ion.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [46]
The variable ion_info is : []
The variable ion_mol2files is : ['SC.mol2']
The variable original_pdb is : ionpair_renum.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 : 3.0
The variable force_field is : ff14SB
The variable frcmod_files is : ['UN1.frcmod', 'UN2.frcmod', 'UN3.frcmod', 'UN4.frcmod']
The variable gaff is : 1
The variable group_name is : ion
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 : ['UN1.mol2', 'UN2.mol2', 'UN3.mol2', 'UN4.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
******************************************************************
* *
*======================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 46 atoms in the large model.
***Check the standard model...
Traceback (most recent call last):
File "/home/ccg3/Downloads/amber18/bin/MCPB.py", line 684, in <module>
premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
File "/home/ccg3/Downloads/amber18/lib/python2.7/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!
The input I am using is:
original_pdb ionpair_renum.pdb
group_name ion
cut_off 3.0
ion_ids 46
ion_mol2files SC.mol2
naa_mol2files UN1.mol2 UN2.mol2 UN3.mol2 UN4.mol2
frcmod_files UN1.frcmod UN2.frcmod UN3.frcmod UN4.frcmod
large_opt 1
Any help would be highly appreciated!
Thanks and regards,
Ritwika
Ritwika Chatterjee
Graduate Student
Computational Chemistry Lab
Department of Organic Chemistry
Indian Institute of Science
Bengaluru - 560012
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Received on Sun Jul 16 2023 - 21:30:02 PDT
