Hi all,
Hi all,
I have done md simulation for my system (ligand-protein complex) with AMBER16 and I would like to do some EDA analysis on it using NAMD energy plugin in VMD. I have tested it according to this short tutorial:
https://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/
And also, changed .nc file into .dcd file but seems there is still some problem with .top file and AMBER parameters. I prefer to run it from TK console but could not find the script template for that.
Any help/suggestion would be appreciated.
Best
Zahra
Hi Zahra,
To run NAMDenergy you need to have namd instaled. Here is a simple script to run NAMDenergy in tcl script
##########################################
mol new {PSF_FILE}.psf
mol addfile {DCD_FILE}.dcd waitfor all
set sel1 [atomselect top " ATOM SELECTION 1 "]
set sel2 [atomselect top " ATOM SELECTION 2 "]
exec ="{YOUR_NAMD_DIR}/namd2"
set prm "{CHARMM_FF_FILE}"
set tempfile "TEMP_file_name"
set outfile "Energy_output_file_name"
package require namdenergy
namdenergy -sel $sel1 $sel2 -exe $exec - par $prm -all -tempname ${tempfile} -ofile ${outfile}
#############################################################
* If you just want self energy of a selection (say sel1) then use only one selection: namdenergy -sel $sel1 -exe $exec - par $prm -all -tempname ${tempfile} -ofile ${outfile}
* insetead of -all you can specify individual energy terms: -bond, -angle, .... as needed:
namdenergy -sel $sel1 -exe $exec - par $prm -bond -angle -vdw -tempname ${tempfile} -ofile ${outfile}
Best,
Subin
Hi Subin,
thanks for your cooment.. I will test it..
Cheers
Zahra
Dear Zhaoxi Sun
Hi.. thanks.. have used cpptraj at the end..
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