* This file is dnainput.inp.
* Usage, charmm <dnainput.inp >dnainput.out.
* Generates coordinate and psf files from pdb file of DNA coordinates.
* Input of DNA with pdb file fixed with fixpdbdna.awk and using top_all27_prot_na.rtf 
*  modified so ADE, CYT, GUA, THY are deoxyribonucleotides in top_all27_prot_dna.rtf. 
* Adjust segment identifier in generate statement to match segid in input file.
*

! Open and read modified rtf and unaltered parameter file.
open read card unit 20 name "top_all27_prot_dna.rtf" 
read rtf card unit 20
close unit 20

open read card unit 20 name "par_all27_prot_na.prm" 
read param card unit 20
close unit 20

! Read sequence from pdb file, generate segment, and read coordinates.
open read card name "1bna.pdb" unit 12
read sequence pdb unit 12
generate DNAA setup first 5ter last 3ter 
rewind unit 12

read coordinate pdb unit 12
close unit 12

! Construct any missing coordinates using ic table. ic table, while preserving ic 
ic fill preserve
ic parameter
ic build
hbuild

! Wite out coordinate and psf files.
open write unit 15 card name 1bnadna.pdb
write coordinates pdb select all end unit 15
* One strand of DNA
*

open write unit 16 card name 1bnadna.psf
write psf card unit 16
* PSF for one strand of DNA
*

stop