#!/bin/bash

## Script will extract the base-pair parameters
## and genereta a plot of each individual base-pair
## using the nastruct command of CPPTRAJ and GNUPLOT
cpptraj='/uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber/bin/cpptraj'

cd ~/gaac/anton/analysis/nastruct

rm BP.*

$cpptraj ../../../GAAC-ions.topo <<EOF
trajin ../../../GAAC-strip.netcdf 1 40000 10
nastruct bp1 naout 1-36.dat resrange 1,36
nastruct bp2 naout 2-35.dat resrange 2,35
nastruct bp3 naout 3-34.dat resrange 3,34
nastruct bp4 naout 4-33.dat resrange 4,33
nastruct bp5 naout 5-32.dat resrange 5,32
nastruct bp6 naout 6-31.dat resrange 6,31
nastruct bp7 naout 7-30.dat resrange 7,30
nastruct bp8 naout 8-29.dat resrange 8,29
nastruct bp9 naout 9-28.dat resrange 9,28
nastruct bp10 naout 10-27.dat resrange 10,27
nastruct bp11 naout 11-26.dat resrange 11,26
nastruct bp12 naout 12-25.dat resrange 12,25
nastruct bp13 naout 13-24.dat resrange 13,24
nastruct bp14 naout 14-23.dat resrange 14,23
nastruct bp15 naout 15-22.dat resrange 15,22
nastruct bp16 naout 16-21.dat resrange 16,21
nastruct bp17 naout 17-20.dat resrange 17,20
nastruct bp18 naout 18-19.dat resrange 18,19
EOF