From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 19 2021 - 12:29:18 CDT
Perhaps there is a discrepancy from topology and params, i.e. autopsf sets
unnecessary impropers while params for them do not exist just because they
are not needed. I wasn't unable to find the requested improper params in
the list of prm and str above files. But I may be easily wrong
francesco
---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Oct 19, 2021, 9:32 AM
Subject: Re: namd-l: impropers for protonated 1-methyladenosine
To: Josh Vermaas <vermaasj_at_msu.edu>
Cc: NAMD <namd-l_at_ks.uiuc.edu>
Hi Josh
Most unfortunately I missed to indicate the full list of parameter files
used, which includes the one that you rightly suggested (the requested
params are of genff type)
par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
toppar_all36_na_modifications.str
toppar_all36_na_rna_modified.str
toppar_all36_prot_arg0.str
toppar_water_ions_namd_adapted.str (I just commented out what namd does not
understand)
this is why I don't understand namd's request (the requested params are
available and unnecessary) and I asked whether namd can be forced to
override psfgen (I used autopsfgen because there are so many chains)
thanks for you care
francesco
On Mon, Oct 18, 2021 at 10:23 PM Josh Vermaas <vermaasj_at_msu.edu> wrote:
> If impropers are defined in the psf, NAMD will expect parameters for
> them. In this case the parameter is in par_all36_cgenff.prm, which goes
> with the top_all36_cgenff.rtf where the B1MA residue is defined.
>
> -Josh
>
> On 10/18/21 3:38 AM, Francesco Pietra wrote:
> > Hello all
> > While attempting minimization of a protein-ribonucleotide containing
> > modified nucleotides, error arose
> >
> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0
> > NG2P1 NG2P1 (ATOMS 4433 4432 4437 4434)
> >
> > These atom types relate, in the given order, to atomnames C6 C5 N1 N6
> > of protonated 1-methyladenosine *resname 1MA in the most recent
> > CHARMM36 psarameterization, Jul21)
> >
> > Added parameters included par_all36_na.prm,
> > ppar_all36_na_rna_modified.str, par_all36_carb.prm. Is any other place
> > from where such impropers are available>
> >
> > Thanks for advice
> > francesco pietra
>
> --
> Josh Vermaas
>
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and
> Molecular Biology
> Michigan State University
> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!tQ1PXRTRF7UXNRkBTP2F0NqsuWXWHcGhbxm3-AcwsEqcQ-2cJnGvc5CIke4d8wqMCw$
>
>
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