I am trying to do a nested loop, but I'm getting the error message "wrong # args: should be "for start test next command". What does this mean, and could someone please help me find what is wrong with my code?
Note: I'm running the code in Virtual Molecular Dynamics (VMD) so it includes some terms specific to the program like resid and mol. Please disregard those.
#count water molecules between chain A and chain C or between #chain B and chain C
set input_file [open ./name_3_pdb_chain_renamed.dat r]
set data [read $input_file]
set data [split $data "\n"]
close $input_file
set chain_list [lindex $data 0]
cd 7_count_water
set outfile [open count_water3.dat w]
set chain_compare ""
set pdblen [llength $chain_list]
for {set i 0} {$i<$pdblen} {incr i}
{
set pid [lindex [lindex $chain_list $i] 0]
set len [llength [lindex $chain_list $i]]
mol load pdb ../2_chain_rename/${pid}_chain_revised.pdb
mol modstyle 0 top NewCartoon
if {$len==4} {
set chain_compare [lappend chain_compare $pid]
}
set 11 [atomselect top all]
set mid [$11 molid]
mol delete $mid
}
set lll [llength $chain_compare]
for {set j 0} {$j< $lll} {incr j}
{
set pid [lindex $chain_compare $j]
mol load pdb ../2_chain_rename/${pid}_chain_revised.pdb
set 11 [atomselect top "chain A and name CA"]
set res_len [llength [$11 get resid]]
set res_id [$11 get resid]
#residue length for chain C
set ag [atomselect top "chain C and name CA"]
set ag_len [llength [$al get resid]]
set ag_id [$al get resid]
#loop water between chain A and chain C
for {set k 0} {$k<$res_len} {incr k}
{
set water_around_a [atomselect top "{resname HOH and {within 5.0 of {chain A and resid [lindex $res_id $k]} and {within 5.0 of chain C}}} "]
set water_around_a_resid [$water_around_a get resid]
set water_around_a_resname [$water_around_a get resname]
#loop antigen residues around water
for {set g 0} {$g < ag_len} {incr g}
{
set ag_around_water [atomselect top "{chain C and {resid [lindex $res_id $g] and {within 5.0 of $water_around_a}}} "]
set ag_around_water resid [$ag_around_water get resid]
set ag_around_water_resname [$ag_around_water get resname]
puts $outfile "$pid [lindex $res_id $k] [lindex [$11 get resname] $k] $ag_around_water_resname A: $water_around_a_resname"
}
}
set 11 [atomselect top "chain B and name CA"]
set res_len [llength [$b11 get resid]]
set res_id [$b11 get resid]
#residue length for chain C
set ag [atomselect top "chain C and name CA"]
set ag_len [llength [$al get resid]]
set ag_id [$al get resid]
for {set k 0} {$k<$res_len} {incr k}
{
set water_around_b [atomselect top "{resname HOH and {within 5.0 of {chain B and resid [lindex $res_id $k]} and {within 5.0 of chain C}}} "]
set water_around_b_resid [$water_around_b get resid]
set water_around_b_resname [$water_around_b get resname]
#loop antigen residues around water
for {set g 0} {$g < ag_len} {incr g}
{
set ag_around_water [atomselect top "{chain C and {resid [lindex $res_id $g] and {within 5.0 of $water_around_b}}} "]
set ag_around_water resid [$ag_around_water get resid]
set ag_around_water_resname [$ag_around_water get resname]
puts $outfile "$pid [lindex $res_id $k] [lindex [$11 get resname] $k] $ag_around_water_resname A: $water_around_b_resname"
}
}
}
close $outfile
cd ..
