VMD-L Mailing List
From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Sep 29 2015 - 12:59:40 CDT
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Hi,
I am trying to write a function that will take in a psf and pdb and then
displace them. Doing this multiple times should make a periodic system of
identical ligands.
proc create_lc_system {masterpsffile masterpdbfile N } {
resetpsf
set dx 20.0;
set segnum 1
for {set i -$N} {$i <=$N } {incr i} {
#read the master file
readpsf $masterpsffile pdb $masterpdbfile
#load the molecule
mol load psf $masterpsffile pdb $masterpdbfile
#only move the newly loaded ligand, so give it a unique segid
set newseg [atomselect top all]
set newsegname "P$segnum"
set newsegid "P$segnum"
$newseg set segname $newsegname
$newseg set segid $newsegname
set atomstomove [atomselect top "segname $newsegname"]
foreach atom [$atomstomove get {segid resid name x y z}] {
foreach {segid resid name x y z} $atom {break}
set newx [expr $x + $i*$dx]
coord $segid $resid $name [list $newx $y $z]
}
incr segnum
}
writepdb lc_system_${N}.pdb
writepsf lc_system_${N}.psf
mol load psf lc_system_${N}.psf pdb lc_system_${N}.pdb
}
When I run it, the script fails on the coord command:
psfgen) no segment P1
ERROR: failed on coord
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
If I use the vmd graphical representations or just picking atoms I see the
segnameand id has been changed. Anyone know what I am doing incorrectly?
Thanks,
Eddie
-- _________________________________________________________ Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad> Assistant Professor of Physics Computational Nanophotonics Southern Illinois University Edwardsville (618) 650-2390
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