From: Ingrid Bernardes Santana Martins (ingrid.martins_at_unesp.br)
Date: Wed Apr 13 2022 - 09:15:15 CDT
Hi! I coud not accept your shared file with my email.
could you send the pdb, psf, and par files directly on e-mail?
thanks
Em ter., 12 de abr. de 2022 às 13:25, (s) Lucy McEvoy <
L.McEvoy-18_at_student.lboro.ac.uk> escreveu:
> 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
>
> ** THIS MESSAGE ORIGINATED OUTSIDE LOUGHBOROUGH UNIVERSITY **
>
> ** Be wary of links or attachments, especially if the email is unsolicited
> or you don't recognise the sender's email address. **
>
> 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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