VMD-L Mailing List

From: Nikhil Maroli (scinikhil_at_gmail.com)
Date: Tue Oct 13 2015 - 00:42:55 CDT

Dear All,
This is my second mail regarding cyclic peptide nanotube psf, i run this
script but i got only one ring in psf and new pdb i wanted to get for full
tube

my system contains 8 rings in each rings 8 amino acids ,i able to make
cyclic peptide
can anyone tell me how to make psf fir cyclic peptide nanotube

package require psfgen
topology top_all36_prot.rtf
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment A {first NONE
last NONE
pdb cpnl.pdb
}
patch LINK A:14 A:1
regenerate angles dihedrals
patch LINK A:15 A:29
regenerate angles dihedrals
patch LINK A:29 A:43
regenerate angles dihedrals
coordpdbcpn.pdb A
guesscoord
writepsf new.psf
writepdb new.pdb

thanks 

-- 
Ragards,
Nikhil Maroli