From: Ingrid Bernardes Santana Martins (ingrid.martins_at_unesp.br)
Date: Mon Apr 11 2022 - 16:56:05 CDT
Hello,
Have you seen if your atom name comparing PSF and PDB file is correct?
It could be this.
Att.
Em seg., 11 de abr. de 2022 às 15:17, (s) Lucy McEvoy <
L.McEvoy-18_at_student.lboro.ac.uk> escreveu:
> 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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