VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Oct 21 2021 - 05:04:03 CDT

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!uK0a09CmE0nYvDYgO4VK9-osLUzUzkFE_ET6iewGZXN3EdYKKRGrd6d8MGvULW4pPw$
>>>> <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!tQ1PXRTRF7UXNRkBTP2F0NqsuWXWHcGhbxm3-AcwsEqcQ-2cJnGvc5CIke4d8wqMCw$>
>>>>
>>>>
>>> --
>>> Josh Vermaas
>>> vermaasj_at_msu.edu
>>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>>> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/ <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!suVYvBxuzd_5oBAh9RiVqStgNkm016ZJInN7MZDvwcLUmoHxNN5Md6xzH7tTLRM5tA$>
>>>
>>>