From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Jan 01 2021 - 00:24:00 CST
Since you're running in debug mode, you should get a namd config file
produced in your working directory. What happens when you try running namd
with that config file?
Best,
Peter
On Fri, Jan 1, 2021 at 12:23 AM Khoualdi Asma Feriel <
asma.feriel.khoualdi_at_umontreal.ca> wrote:
> 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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