Re: Dihedral parameters for terminal alkyne

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Sun Dec 12 2021 - 13:53:40 CST

Hi Fabrice.

Thanks for the suggestion.

I don't think this would solve the problem as the data requested by Namd
2.14 is not included in the CGenFF parameters/topology files.

Also, following Michael Robinson's suggestion, I inserted dihedral
parameters with an equilibrium angle of 0 and a strength of 0, which solved
the problem.

Anyway, thanks for the help.

Best wishes.

Denilson.

Em seg., 6 de dez. de 2021 às 02:32, Fabrice Gardebien <
fabrice.gardebien_at_univ-reunion.fr> escreveu:

> Dear Dennilson,
>
> I am not sure whether this could solve your problem but have you tried to
> tick the option " Include parameters that are already in CGenFF" in
> generating your STR file?
>
> Best wishes.
> On 05/12/2021 22:53, DENILSON FERREIRA DE OLIVEIRA wrote:
>
> Dear all,
>
> 1) The C3_WIN-1-COR.str file was generated for an organic substance, using
> the CHARMM General Force Field (CGenFF) program version 2.5, through the
> Paramchem website (https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!DZ3fjg!ugrRDAgoCMT0aUbi6k1ylKk_tih9cjoOeKLQWD87o-WMMwhdJUMxvfqxBEIU8UqY6Q$
> <https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;%21%21DZ3fjg%21r7TXiOBr_-a2sDPPFdaSlwVkONXiVoumQ25REM534_RqlbdCV3b9vi9PM9pbFg7WUg$>
> )
>
> 2) Using the topology files contained in toppar_c36_jul21.tgz, which is
> available through the MacKerell Lab Homepage (
> https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*charmm__;Iw!!DZ3fjg!ugrRDAgoCMT0aUbi6k1ylKk_tih9cjoOeKLQWD87o-WMMwhdJUMxvfqxBEKYKRBOKA$
> <https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*charmm__;Iw%21%21DZ3fjg%21r7TXiOBr_-a2sDPPFdaSlwVkONXiVoumQ25REM534_RqlbdCV3b9vi9PM9pbBsvQnw$>),
> as well as the C3_WIN-1-COR.str file generated in Paramchem, I prepared the
> pdb and psf files using VMD 1.9.4a55.
>
> 3) In the configuration file to carry out calculations with Namd 2.14 I
> have provided all the parameter files in the order that seems correct to
> me. The following is observed in the output from Namd:
>
> "...
> Info: COORDINATE PDB ./6vxx_C3_WIN-1_autopsf.pdb
> Info: STRUCTURE FILE ./6vxx_C3_WIN-1_autopsf.psf
> Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS ./par_all36m_prot.prm
> Info: PARAMETERS ./par_all36_lipid.prm
> Info: PARAMETERS ./par_all36_carb.prm
> Info: PARAMETERS ./par_all36_na.prm
> Info: PARAMETERS ./par_all36_cgenff.prm
> Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str
> Info: PARAMETERS ./toppar_water_ions_namd.str
> Info: PARAMETERS ./C3_WIN-1-COR.str
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Info: SKIPPING rtf SECTION IN STREAM FILE
> Info: SKIPPING rtf SECTION IN STREAM FILE
> Info: SKIPPING rtf SECTION IN STREAM FILE
> "
>
> 4) However, Namd 2.14 did not perform the calculations because it
> encountered an error:
>
> "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CG3RC1 CG3C50 CG1T1
> CG1T2 (ATOMS 53401 53404 53407 53408)"
>
> 5) It is clear to me that this error is due to the fact that there is no
> parameter for dihedral angles of atoms of the terminal alkyne function
> anywhere:
>
> CG1T2 : C(sp1) terminal
> CG1T1 : C(sp1) non-terminal
> CG3C50 : C(sp3) linked to CG1T1
> CG3RC1 : C(sp3) linked to CG3C50
>
> 6) To be clearer, I could not find data for the dihedral angle CG3RC1
> CG3C50 CG1T1 CG1T2 anywhere in the topology and parameter files listed in
> item "3" of this message.
>
> 7) In fact, it seems to me that there is no point in working with a
> dihedral angle for such atoms.
>
> 8) Consequently, I will be grateful if anyone can be kind enough to make a
> suggestion to solve the problem.
>
> Thanks.
>
> Denilson.
>
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