Re: Didn't find vdW parameter for stop type HB1 Error

From: s) Lucy McEvoy (L.McEvoy-18_at_student.lboro.ac.uk)
Date: Tue Apr 12 2022 - 11:25:13 CDT

Hi,

One difference I have spotted is that there is 1x HB1 in my PDB, as copied below

ATOM 8 HB1 SER A 1 -26.650 24.346 80.716 1.00 0.00 AP1

but there are multiple in my PSF (made through auto psfgen), such as the examples below

6 AP1 1 SER HA HB1 0.100000 1.0080 0
7 AP1 1 SER CB CT2 0.050000 12.0110 0
8 AP1 1 SER HB1 HA2 0.090000 1.0080 0

Is this correct? Are they named differently like you suggested?

Also have an error of 'ABNORMAL EOF FOUND _ beffer=*END* which I can see is common online, I have done the suggestions to check that all input files end with 'END' but still appears.

Thanks for any help
Lucy

From: Ingrid Bernardes Santana Martins <ingrid.martins_at_unesp.br>
Date: Monday, 11 April 2022 at 22:56
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>, (s) Lucy McEvoy <L.McEvoy-18_at_student.lboro.ac.uk>
Subject: Re: namd-l: Didn't find vdW parameter for stop type HB1 Error

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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 ŕs 15:17, (s) Lucy McEvoy <L.McEvoy-18_at_student.lboro.ac.uk<mailto: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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