Dihedral parameters for terminal alkyne

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Sun Dec 05 2021 - 12:53:41 CST

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!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!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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