VMD-L Mailing List

From: Lee, Hwan Kyu (NIH/NHLBI) [E] (leeh3_at_nhlbi.nih.gov)
Date: Tue Feb 24 2009 - 19:09:27 CST

Dear VMDer,

I calculated center of mass for each residue, and then calculated dihedral angles for those four center of mass. I wrote tcl script like below, but got an error, "expected integer but got "11.965297699" measure dihed: bad atom index". It looks like $sel11 cannot be recognized as a coordinate of COM. How can I fix this problem?
Thanks for your help in advance.

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set numFrames [molinfo top get numframes]

for {set pp 300} {$pp < $numFrames} {incr pp} {

        set n 1

        while {$n < 35} {

        set n1 [expr {$n+1}]
        set n2 [expr {$n+2}]
        set n3 [expr {$n+3}]

        set sel1 [atomselect top "resid $n"]
        set sel2 [atomselect top "resid $n1"]
        set sel3 [atomselect top "resid $n2"]
        set sel4 [atomselect top "resid $n3"]

        set sel11 [measure center $sel1 weight mass]
        set sel21 [measure center $sel2 weight mass]
        set sel31 [measure center $sel3 weight mass]
        set sel41 [measure center $sel4 weight mass]

        set dih [measure dihed [list $sel11 $sel21 $sel31 $sel41]]

        $sel1 delete
        $sel2 delete
        $sel3 delete
        $sel4 delete
        $sel11 delete
        $sel21 delete
        $sel31 delete
        $sel41 delete

        incr n
        set result [open "dihedral.xvg" a]
        puts $result "$dih"
        close $result
        }
}
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best,
Hwankyu.