Re: Fwd: impropers for protonated 1-methyladenosine

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Oct 20 2021 - 05:41:20 CDT

I repeated autopsfgen scratch, this time erasing all default topology files
in autopsfgen before adding topologies from
toppar_c36_jul21 (newly taken from Mackerell web site), plus my own
ligand.str

top_all36_lipid.rtf/home/francesco/softw/CHARMM_FF/toppar_c36_jul21
> top_all36_na.rtf
> toppar_all36_prot_arg0.str
> toppar_all36_na_rna_modified.str
> toppar_water_ions_namd_adapted.str
> ligand.str
>

Then, I repeated minimization from scratch adding params from

> toppar_c36_jul21 (newly taken from Mackerell web site)
>
par_all36_carb.prm
par_all36_cgenff.prm
par_all36_lipid.prm
par_all36m_prot.prm
par_all36_na.prm
plus the above .str

Same error as before. This time any mixing with top/par is absolutely ruled
out

Info: SKIPPING rtf SECTION IN STREAM FILE
> Info: SUMMARY OF PARAMETERS:
> Info: 1227 BONDS
> Info: 3939 ANGLES
> Info: 10859 DIHEDRAL
> Info: 280 IMPROPER
> Info: 6 CROSSTERM
> Info: 403 VDW
> Info: 103 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1
> NG2P1 (ATOMS 4433 4432 4437 4434)
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2R64 CG2RC0 NG2P1
> NG2P1 (ATOMS 4433 4432 4437 4434)
>

Whether my mistake or intrinsic problems, I am stuck

thanks for advice
francesco

On Tue, Oct 19, 2021 at 8:03 PM Josh Vermaas <vermaasj_at_msu.edu> wrote:

> 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>
> 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!uGX6MySUjWBm360WO5eAk2b6JJAYghHwzVvxBw-NXWR5XlaypVXK0Uvdmt9_tyd_sw$
>> <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!tQ1PXRTRF7UXNRkBTP2F0NqsuWXWHcGhbxm3-AcwsEqcQ-2cJnGvc5CIke4d8wqMCw$>
>>
>>
> --
> Josh Vermaas
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/
>
>

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