From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Oct 21 2021 - 07:56:06 CDT

I do not understand 'pass through cgenff'

On Thu, Oct 21, 2021, 12:04 PM Ashar Malik <asharjm_at_gmail.com> wrote:

> Haven’t followed the full thread here. Sorry if my answer repeats
> something or is completely off.
>
>
>
> If you have to add parameters (which is what the error is about) - perhaps
> you could pass your “molecule” through cgenff? And get a guess from there.
> And then for the same dihedral parameters match yours (the one you use (42
> 0 0) and see if the values are similar? If yes, it’s still not
> “completely” safe but more safe then “completely” unsafe. If the values are
> off, then perhaps there is reason to be worried :)
>
>
>
>
> On Thu, 21 Oct 2021 at 5:50 PM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> 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!qVK3y0oXsevKjYRsivSWC3v-hE1VO81bjoEH2xTL5AX53vUydPgcyktzpoTr6O5Lyg$
>>>>> <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!tQ1PXRTRF7UXNRkBTP2F0NqsuWXWHcGhbxm3-AcwsEqcQ-2cJnGvc5CIke4d8wqMCw$>
>>>>>
>>>>>
>>>> --
>>>> Josh Vermaas
>>>> vermaasj_at_msu.edu
>>>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>>>> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/ <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!suVYvBxuzd_5oBAh9RiVqStgNkm016ZJInN7MZDvwcLUmoHxNN5Md6xzH7tTLRM5tA$>
>>>>
>>>>