From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Mon Dec 06 2021 - 05:45:42 CST
Hi Denilson,
If the dihedral for a specific interaction is undefined, such as around the
linear atoms of your triple bond, some MD packages will require a dihedral
value with a strength of 0, and others won't require a dihedral at all.
CHARMM does not require a dihedral value for these instances, but NAMD
does; CGenFF is set up for CHARMM, and so will not output a dihedral in
these cases. In the case of an undefined dihedral in NAMD, you can simply
add a parameter with an equilibrium angle of 0 and a strength of 0 - it
won't affect the results in any way, but is required to run NAMD in these
cases.
Regards,
Michael Robinson
On Mon, 6 Dec 2021 at 05:58, DENILSON FERREIRA DE OLIVEIRA <denilson_at_ufla.br>
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!vpC3LLjbPFGJ9Czo7ZfxGkt-FQ16kH2b7BFx46m7ETQJcP7QGprivIjJWry1lucaow$
> <https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!DZ3fjg!r7TXiOBr_-a2sDPPFdaSlwVkONXiVoumQ25REM534_RqlbdCV3b9vi9PM9pbFg7WUg$>
> )
>
> 2) Using the topology files contained in toppar_c36_jul21.tgz, which is
> available through the MacKerell Lab Homepage (
> https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*charmm__;Iw!!DZ3fjg!vpC3LLjbPFGJ9Czo7ZfxGkt-FQ16kH2b7BFx46m7ETQJcP7QGprivIjJWrxH4xW3pQ$
> <https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*charmm__;Iw!!DZ3fjg!r7TXiOBr_-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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