VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Oct 21 2021 - 04:15:56 CDT

Having no answer, I choose the shortest route to bypass the error, i.e., I
added
"CG2R64 CG2RC0 NG2P1 NG2P1 42.00 0 0.00 ! 34HC, from 3MCn, yxu,
TO BE OPTIMIZED, RNA"
to par_all36_cgen.prm, renamed par_all36_cgen_MOD.prm

Minimization went on correctly, no conflict came out.

May I ask whether there could anything unsafe on going on following this
shortcut?
thanks
francesco pietra

On Wed, Oct 20, 2021 at 4:14 PM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Forwarding to VMD, which is also concerned
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Wed, Oct 20, 2021 at 12:41 PM
> Subject: Re: Fwd: namd-l: impropers for protonated 1-methyladenosine
> To: Josh Vermaas <vermaasj_at_msu.edu>
> Cc: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> 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!vsrV4BVUCcVaWTUaEar6FDgyoGVefHV6qGx07rtYVvuJ3gPSm1YtrnKLEAk_DLtcUA$
>>> <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!tQ1PXRTRF7UXNRkBTP2F0NqsuWXWHcGhbxm3-AcwsEqcQ-2cJnGvc5CIke4d8wqMCw$>
>>>
>>>
>> --
>> Josh Vermaas
>> vermaasj_at_msu.edu
>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/ <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!suVYvBxuzd_5oBAh9RiVqStgNkm016ZJInN7MZDvwcLUmoHxNN5Md6xzH7tTLRM5tA$>
>>
>>