From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Mon Oct 18 2021 - 15:23:30 CDT
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!rTtit1Fs-jv9-w5brWl3U2LIMMx0OSW90qwYl2LvlBh0FSGhnTWhewlN7H8-7ET2fw$
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