From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Wed Dec 08 2021 - 07:06:18 CST
Dear Michael Robinson,
Thank you very much.
Denilson
Em seg., 6 de dez. de 2021 às 08:45, Michael Robinson <
michael.robinson1_at_monash.edu> escreveu:
> 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!qbO3aULYRNRrBmpdN2QzX8LoKemjQmLy7R6IR6os1Vbl8zQ2gjsH3vq8Mh75MHwm0A$
>> <https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!DZ3fjg!r7TXiOBr_-a2sDPPFdaSlwVkONXiVoumQ25REM534_RqlbdCV3b9vi9PM9pbFg7WUg$>
>> )
>>
>> 2) Using the topology files contained in toppar_c36_jul21.tgz, which is
>> available through the MacKerell Lab Homepage (
>> https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*charmm__;Iw!!DZ3fjg!qbO3aULYRNRrBmpdN2QzX8LoKemjQmLy7R6IR6os1Vbl8zQ2gjsH3vq8Mh5elGMALw$
>> <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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>
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