From: Sonibare, Kolawole (kasonibare42_at_students.tntech.edu)
Date: Tue May 15 2018 - 17:32:32 CDT
Dear NAMD users,
I am a new NAMD user and I intend to run a simulation of 120 molecules of an organic compound. Using some examples, I have been able to generate just a single molecule using psfgen. Please, how can I use this to get 120 molecules? I have attached my tcl script.
package require psfgen
topology plant.top
set name 2units
resetpsf
segment li {
residue 1 SYR
residue 2 GUAI
}
patch 4O5 li:1 li:2
regenerate angles dihedrals
coordpdb plant.pdb
guesscoord
writepdb $name.pdb
writepsf $name.psf
exit
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