EasyConsoleTool
A TCL VMD Program for the easy and flexible trajectory analysis.
AUTHOUR
ANJI BABU KAPAKAYLA
IIT KANPUR, INDIA.
anjibabu480@gmail.com
USAGE
source ECT.tcl in VMD tk console
Commands available
my_commnds: Prints available commands on the console
Alignment, RMSD ,distance, angle, dihedral, contact_map
clustering, details, count_waters, HBonds, pbs_box,
save_pdb, save_image, sasa, save_coordinates, bgcolor
HB_occupancy, show_interactions, show_hbonds,count_hbonds
--help
Examples
my_commands : Shows all available commands
--help
Gives details of any mentioned command
USAGE : --help command
example : --help distance
example : --help angle
save_pdb
Writes pdb file for given options
USAGE : save_pdb atomselection start_frame end_frame stride molid filename
EXAMPLE : save_pdb "protein" 5 100 5 top file.pdb
Above example , It will write file.pdb for "protein" from frame 5 to 100 by skipping every 5 frames.
Align
align molid1 molid2
example : align 0 1
RMSD
Measures Avg.RMSD & std for given selections
USAGE : rmsd Atomselection molid1 molid2
example : rmsd "backbone" top 1
example : rmsd "protein" top top
IF both the molids are same , RMSD will be calculated by taking zeroth frame as reference
distance
Measures Distance, Avg Distance & std for any given 2 atoms
USAGE : distance sel1 sel2 <initial-frame> <end-frame> <-show_plot>
example : distance "serial 3418" "serial 3415"
example : distance "serial 3418" "serial 3415" 100 2000
example : distance "serial 3418" "serial 3415" -show_plot
example : distance "serial 3418" "serial 3415" 10 1000 -show_plot
OUTPUT : DISTANCE.xvg and dist.png
angle
Measures Avg. angle & std for any given 3 atoms
USAGE : angle sel1 sel2 sel3
example : angle "serial 3418" "serial 3415" "serial 3395"
OUTPUT : ANGLE.dat
dihedral
Measures Avg Dihedral angle & std for any given 4 atoms
USAGE : dihedral sel1 sel2 sel3 sel4
example : dihedral "serial 3418" "serial 3415" "serial 3412" "serial 3395"
example2 : dihedral "index 3417" "index 3414" "index 3411" "index 3394"
OUTPUT : DIHEDRAL.dat
show_residues
Prints RESID and corresponding RESNAME for given selection and for given frames
USAGE : show_residues sel molid <initial frame> <final frame>
example : show_residues "resid 170 to 180" 0 0 5
example2 : show_residues "(not resname WAT) and within 3 of resid 235" 0 5 10
example3 : show_residues "protein and hydrophobic " 0 1 0
OUTPUT : RESNAMES.dat
details
Prints required molecular details for given molid
USAGE : details molid
example : details 0
count_waters
Prints Avg. No of waters present around given selection
USAGE : count_waters sel molid start_frame end_frame
Example : count_waters "within 5 of resid 235" 0 5 10
OUTPUT : NO-OF-WATERS.dat
Anji Babu Kapakayala