Didn't find vdW parameter for stop type HB1 Error

From: s) Lucy McEvoy (L.McEvoy-18_at_student.lboro.ac.uk)
Date: Mon Apr 11 2022 - 13:14:45 CDT

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Hi,

I have tried to run a simulation on my PDB and PSF files however I am getting the following error

‘Didn't find vdW parameter for stop type HB1’

I have seen this error online before and solutions have been regarding the parameter files used.
The parameters files I have included in the configuration file are the following:
Par_all27_prot_lipid.inp
Par_all36_carb.prm
Par_all36_cgneff.prm
Par_all36_na.prm
Par_all36m_prot.prm
Toppar_water_ions_.namd.str

Looking through them, HB1 is in ‘Par_all36m_prot.prm’ file so I am unsure why it isn’t being picked up? I have tried multiple combinations of the files to see if any affect each other but have had no success.

Any help would be greatly appreciated.

Many thanks
Lucy

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