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From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Fri Jan 04 2013 - 11:17:30 CST

Hi, I quickly wrote this script that I was hoping would perform the following function: align each phosphorylated residue in a peptide with a ligand in a crystal structure and loop through frames in a trajectory measuring contacts between the simulated peptide and the protein its "bound" to. This seemed simple enough, but I'm running into all kinds of problems... The output file only contains the info from the last frame, the "tempsel" atomselection does not seem to be updating (or at least the alignment I'm doing doesn't work. Finally, it does not seem to actually be closing the files that I label as "outfile" and I get this error: couldn't open "contactstest4.csv": too many open files

If anyone enjoys writing TCL scripts for trajectory analysis and would like to help me with this troubleshooting I'd appreciate it! I thought this was really straightforward...

set filename "contactstest"
puts $filename
set cutoff 1
set numfr [molinfo $traj get numframes]
set firstframe 0
set findP [atomselect $traj "protein and name P"]
set Pres [$findP get resid]
set mv [atomselect $traj all]
set wd40 [atomselect $reference "chain D"]
set refsel [atomselect $reference "chain F and resid 4 and name P OG1 or resid 5 and name N CA CG"]
set lastframe [expr {$numfr-1}]
puts "last frame: $lastframe"

        set n 1
        foreach j $Pres {
                incr n
                set j2 [expr {$j+1}]
                set tempsel [atomselect $traj "protein and resid $j and name P OG or resid $j2 and name N CA CG"]
                                puts "test $j"
                for {set i $firstframe} {$i < $numfr} {incr i} {
                        puts "testA $i"
                        set outfile [open $filename$n.csv w]
                        $tempsel frame $i
                        set M [measure fit $tempsel $refsel]
                        $mv move $M
                        set tempsel2 [atomselect $traj "protein and noh"]
                        set tmp [measure contact $cutoff $wd40 $tempsel2]
                        set tmp2 [llength [lindex $tmp 0]]

                        puts $outfile "$i, $tmp2"

                        }
                        close $outfile
                        }

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