*FILENAME: gen-alpha.inp
*PURPOSE: generate alpha helix
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
*
! Unix environment variable CHM_HOME should point to the charmm installation directory

read rtf card name $CHM_HOME/toppar/top_all22_prot.inp
read para card name $CHM_HOME/toppar/par_all22_prot.inp

read sequence card
* just a test sequence
*
9
ALA GLY MET PHE ILE ILE
LEU VAL SER

gene hlx setup ! setup keyword need to get IC tables
ic purge ! remove unused entries (at ends)
! fill ic table with bondlengths and angles from parameter file
! could also
ic param

! now fix the backbone dihedrals in alpha helix conformation
set 1 1
set 2 @1
set 3 @1
incr 2 by 1
incr 3 by 2

label loop
ic edit
dihe @1 C @2 N @2 CA @2 C -57. !PHI
dihe @2 N @2 CA @2 C @3 N -47. !PSI
end
incr 1 by 1
incr 2 by 1
incr 3 by 1
if 3 le 9 goto LOOP

! construct cartesian coordinates from the internal coordinates
! this will make alpha helical backbone, and extended sidechains

ic seed hlx 1 N hlx 1 CA hlx 1 C
ic build
write coor pdb name helix.pdb
* simple helix built in CHARMM
*
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden