Re: Fwd: impropers for protonated 1-methyladenosine

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Tue Oct 19 2021 - 13:03:04 CDT

You didn't happen to mix a topology file from toppar_c36_jul20 with a
parameter file from toppar_c36_jul21, did you? In the July 2020 release,
there is a line like this in par_all36_cgenff.prm:

CG2R64 CG2RC0 NG2P1  NG2P1     42.00  0     0.00 ! 34HC, from 3MCn, yxu,
TO BE OPTIMIZED, RNA

This corresponds to the improper definition in that version of the force
field. "IMPR C6   C5   N1   N6" In the 2021 release, the order in the
improper is different "IMPR C6   N1   N6   C5", so the parameter that
would be looked up also changes:

CG2R64 NG2P1  NG2P1  CG2RC0    52.00  0     0.00 ! ADEp, B1MA, from 3MC,
yxu, TO BE OPTIMIZED, RNA

To be honest, I hadn't realized that changes like this happened, but in
this case it is all laid out in toppar_all.history:

"!following removed due to conflict
CG2R64 CG2RC0 NG2P1  NG2P1     42.00  0     0.00 ! B1MA, yxu, TO BE
OPTIMIZED, RNA
CG2R64 CG2R61 NG2P1  NG2P1     42.00  0     0.00 ! from CG2R64 CG2RC0
NG2P1  NG2P1
CG2R64 CG2R62 NG2P1  NG2P1     42.00  0     0.00 ! B3MC, yxu, TO BE
OPTIMIZED, RNA
!which will be treated with
CG2R64 NG2P1  NG2P1  CG2R62    52.00  0     0.00 ! CYTp, yxu, TO BE
OPTIMIZED, RNA
CG2R64 NG2P1  NG2P1  CG2R61    52.00  0     0.00 ! CYTp, yxu, TO BE
OPTIMIZED, RNA
CG2R64 NG2P1  NG2P1  CG2RC0    52.00  0     0.00 ! ADEp, from 3MC, yxu,
TO BE OPTIMIZED"

-Josh

On 10/19/21 1:29 PM, Francesco Pietra wrote:
> 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
> <mailto: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 <mailto:vermaasj_at_msu.edu>>
> Cc: NAMD <namd-l_at_ks.uiuc.edu <mailto: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
> <mailto: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 <mailto: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!qNT4ZozbCnn8bUfxdAuMtyVkLckSj-chLESEsk9oXna7Kt5KESWU32r_Ts7Pw0NFAg$
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>

-- 
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!qNT4ZozbCnn8bUfxdAuMtyVkLckSj-chLESEsk9oXna7Kt5KESWU32r_Ts7Pw0NFAg$ 

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