Generating parameters for chlorophyll a - 03/21/22 09:47 PM

Hi,

I'm working on the CHARMM tutorial : http://mackerell.umaryland.edu/cgenff_dwld.php with chlorophyll a in order to calculate the water interaction energies. Like suggested in the paper J Mol Graph Model. 2015 May;58:30-9. doi: 10.1016/j.jmgm.2015.03.001 Epub 2015 Mar 10. Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. Guerra F1, Adam S1, Bondar AN2

I removed the phytyl chain and replaced the side chains by hydrogens.

I used CHARMM-GUI pdb reader tool to get the .prm and .rtf files of the molecule and use them to build my toppar stream file.

Using CHARMM program I was able to get the Gaussian input file .gjf, and it's actually running.

I'm wondering how to get the other Gaussian input files ? (e.g tdaz_water_hf_H1.gjf) I understand that the coordinates are the ones obtain after the Gaussian geometry optimization but I don't understand how the bonds, angles and dihedrals are set up ?

In the input file water_constr.inp I'm also wondering how the IC table is set up, so as the new stream toppar file with modified partial charges.

Thanks a lot,

Martina

Edit : my Gaussian run just failed with this error message, how can I solve this issue ? :

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Restarting incremental Fock formation.

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Restarting incremental Fock formation.

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

>>>>>>>>>> Convergence criterion not met.

SCF Done: E(RHF) = -1331.89533482 A.U. after 129 cycles

NFock=128 Conv=0.14D-04 -V/T= 2.0009

Convergence failure -- run terminated.

I'm working on the CHARMM tutorial : http:/

I removed the phytyl chain and replaced the side chains by hydrogens.

I used CHARMM-GUI pdb reader tool to get the .prm and .rtf files of the molecule and use them to build my toppar stream file.

Using CHARMM program I was able to get the Gaussian input file .gjf, and it's actually running.

I'm wondering how to get the other Gaussian input files ? (e.g tdaz_water_hf_H1.gjf) I understand that the coordinates are the ones obtain after the Gaussian geometry optimization but I don't understand how the bonds, angles and dihedrals are set up ?

In the input file water_constr.inp I'm also wondering how the IC table is set up, so as the new stream toppar file with modified partial charges.

Thanks a lot,

Martina

Edit : my Gaussian run just failed with this error message, how can I solve this issue ? :

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Restarting incremental Fock formation.

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Restarting incremental Fock formation.

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

>>>>>>>>>> Convergence criterion not met.

SCF Done: E(RHF) = -1331.89533482 A.U. after 129 cycles

NFock=128 Conv=0.14D-04 -V/T= 2.0009

Convergence failure -- run terminated.