From: Nadira Khatoon (Nadira.Khatoon_at_bioschool.iitd.ac.in)
Date: Mon May 24 2021 - 09:26:49 CDT
Thanks for the help René. Your suggestion solved the issue. However, now
I am getting a new error stating, "FATAL ERROR: UNABLE TO FIND DIHEDRAL
PARAMETERS FOR CTL2 OSL PL OSL (ATOMS 17 23 20 24)". This gets solved if
I use toppar_all36_lipid_sphingo.str as one of my parameter file in
addition to the par_all36_lipid.prm , par_all36m_prot.prm, and
toppar_water_ions.str.
I am unable to understand the reason behind it. Will unnecessary
parameter file affect simulation results?
-------- Original Message --------
Subject: Re: namd-l: Regarding Parameter file
Date: 24.05.2021 14:21
From: René Hafner TUK <hamburge_at_physik.uni-kl.de>
To: namd-l_at_ks.uiuc.edu, Nadira Khatoon
<Nadira.Khatoon_at_bioschool.iitd.ac.in>
Hi,
ON3 is an atom type from par_all36_na.prm
Inside toppar_water_ions.str you only need to comment out any
NBFIXes Lines where "ON3" occurs; may happen for more atom types but
should be solvable the same way.
Cheers
René
On 5/23/2021 7:14 PM, Nadira Khatoon wrote:
> Hi,
> I am new at learning NAMD for simulating membrane embedded proteins.
> Will use of different versions of Charmm parameter files cause errors
> in the simulation?
> Also, an error stating "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM
> TYPE ON3", is coming, but there are no ON3 atoms in both pdb and psf
> files. I am unable to find a solution to this. Could you please help me
> with this?
> For running this simulation, I have used parameter files as mentioned
> below:
> parameters par_all36_lipid.prm
> parameters par_all36m_prot.prm
> parameters toppar_water_ions.str
>
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