From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue May 15 2018 - 18:18:25 CDT
Hi Sonibare,
Put it in a loop.
package require psfgen
topology plant.top
set name 2units
mol new plant.pdb
set sel [atomselect top "all"]
for { set i 0 } { $i < 120 } { incr i } {
resetpsf
segment L$i {
residue 1 SYR
residue 2 GUAI
}
patch 4O5 L$i:1 L$i:2
$sel set segname L$i
$sel moveby [list 1 1 1]
$sel writepdb tmp.pdb
regenerate angles dihedrals
coordpdb L$i tmp.pdb
}
guesscoord
writepdb $name.pdb
writepsf $name.psf
Just out of curiosity, which parameter set are you using for your lignin? You will probably also want to add a patch to both residues to modify the chemistry attached to C1.
-Josh
On 2018-05-15 16:37:59-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
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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