From: Khoualdi Asma Feriel (asma.feriel.khoualdi_at_umontreal.ca)
Date: Thu Dec 31 2020 - 22:29:18 CST
I used the following script to calculate the electrostatic energy but the output file gives me only the column header without any values for frames or energy or anything, I'd appreciate input.
set nfiles 144
set str /lustre04/scratch/asma97/charmm-gui-8960705840/namd/step5_charmm2namd.psf
set TITLE_FIRST step
set TITLE_SECOND _production.dcd
mol new $str type psf waitfor all
for {set j 7} {$j <= $nfiles} {incr j} {
mol addfile /lustre04/scratch/asma97/charmm-gui-8960705840/namd/$TITLE_FIRST$j$TITLE_SECOND type dcd waitfor all
}
set RESIDUE [atomselect top "resid 96 and protein"]
set LIGAND [atomselect top "resid 174 and not water and not protein"]
package require namdenergy 1.4
namdenergy -elec -sel $RESIDUE $LIGAND -keepforce -timemult 2 -updatesel -debug -cutoff 12 -switch 10 -pme -tempname "namd" -ofile "namdEnergy.txt" -exe /home/asma97/.licenses/namd-multicore -timemult 2 -par toppar/par_all36m_prot.prm -par toppar/par_all36_na.prm -par toppar/par_all36_carb.prm -par toppar/par_all36_lipid.prm -par toppar/par_all36_cgenff.prm -par toppar/par_interface.prm -par toppar/toppar_all36_nano_lig.str -par toppar/toppar_all36_nanolig_patch.str -par toppar/toppar_all36_synthetic_polymer.str -par toppar/toppar_all36_synthetic_polymer_patch.str -par toppar/toppar_all36_polymer_solvent.str -par toppar/toppar_water_ions.str -par toppar/toppar_dum_noble_gases.str -par toppar/toppar_ions_won.str -par toppar/toppar_all36_prot_arg0.str -par toppar/toppar_all36_prot_c36m_d_aminoacids.str -par toppar/toppar_all36_prot_fluoro_alkanes.str -par toppar/toppar_all36_prot_heme.str -par toppar/toppar_all36_prot_na_combined.str -par toppar/toppar_all36_prot_retinol.str -par toppar/toppar_all36_prot_modify_res.str -par toppar/toppar_all36_na_nad_ppi.str -par toppar/toppar_all36_na_rna_modified.str -par toppar/toppar_all36_lipid_bacterial.str -par toppar/toppar_all36_lipid_cardiolipin.str -par toppar/toppar_all36_lipid_cholesterol.str -par toppar/toppar_all36_lipid_dag.str -par toppar/toppar_all36_lipid_inositol.str -par toppar/toppar_all36_lipid_lps.str -par toppar/toppar_all36_lipid_miscellaneous.str -par toppar/toppar_all36_lipid_model.str -par toppar/toppar_all36_lipid_prot.str -par toppar/toppar_all36_lipid_sphingo.str -par toppar/toppar_all36_lipid_yeast.str -par toppar/toppar_all36_lipid_hmmm.str -par toppar/toppar_all36_lipid_detergent.str -par toppar/toppar_all36_lipid_ether.str -par toppar/toppar_all36_carb_glycolipid.str -par toppar/toppar_all36_carb_glycopeptide.str -par toppar/toppar_all36_carb_imlab.str -par toppar/toppar_all36_label_spin.str -par toppar/toppar_all36_label_fluorophore.str -par toppar/toppar_all36_lipid_cationpi_wyf.str
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