From: jiali wang (jialiwangnamd_at_gmail.com)
Date: Fri Feb 12 2021 - 23:54:43 CST
Dear NAMD users,
I have an error when I calculate the dihedral angle, the calculation
performed in the VMD. code as below, but it says "expected integer but got
"$sel1" measure dihed: bad atom index". Do you know what happened?
Thank you so much!!
Jiali
set selA [atomselect top "segname PP5 and name C"]
set selB [atomselect top "segname PP5 and name CA"]
set selC [atomselect top "segname PP5 and name CB"]
set selD [atomselect top "segname PP5 and name CG"]
set sel1 [[atomselect top "$selA"] get index]
set sel2 [[atomselect top "$selB"] get index]
set sel3 [[atomselect top "$selC"] get index]
set sel4 [[atomselect top "$selD"] get index]
set nf [molinfo top get numframes]
set outfile [open dihed-cal.dat w]
for {set i 0} {$i < $nf} {incr i} {
puts "frame $i of $nf"
set dihedlist [measure dihed {$sel1 $sel2 $sel3 $sel4}]
puts $outfile "$i $dihedlist"
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