From: jose correa (corrjose_at_gmail.com)
Date: Tue Mar 03 2009 - 20:36:24 CST
Dear NAMD users
I have a big *dcd file (10 GB), then, i can not open it in vmd, looking
about the same problems, i applied the next scrip that was suggested in this
forum, however, after run it in vmd Tk console show: can not read "nf" no
such variable, unable to load structure file dry_prot.psf, can not reat nf"
no such variable, invalid command. Any suggestion?, please.
mol load psf solvated.psf
for {set i 0 } {$i < $nf } {incr i 100 } {
animate read dcd md0001.dcd beg i end i
set sel [atomselect top protein]
$sel writepdb $i.pdb
if { $i == 0 } {
$sel writepsf dry_prot.psf
}
$sel delete
animate delete all
}
mol delete top
mol load psf dry_prot.psf
for {set i 0 } {$i < $nf } {incr i 100 } {
animate read pdb $i.pdb
file delete $i.pdb
}
animate write dcd {myprotein_prot.dcd} waitfor all
best wishes
j correa-basurto
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