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From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Wed Jan 08 2014 - 06:40:10 CST

Many thanks for your help Ajasja, Josh and Mike. Best regards, Flavio On Tuesday, January 7, 2014 6:22 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote: Hi Flavio, Your order of operations is a bit wonky. You've set the variable sasa, and then never update inside the loop. Try the following instead: set fp [open "SASA-output.dat" w] set nf [molinfo top get numframes] set sel [atomselect top "protein and noh"] for { set i 0 } { $i < $nf } { incr i } {     $sel frame $i set sasa [measure sasa 1.40 $sel -restrict] puts $fp "$i $sasa" } close $fp -Josh Vermaas On 01/07/2014 12:40 PM, flavio seixas wrote: Hi, I am trying to generate a file containing Solvent Acessible Surface Area from each frame of the trajectory. I search in VMD list and user guide and I build the following script, which was sourced after loading pdb and dcd files: #sasa calculation loop set fp [open "SASA-output.dat" w] set nf [molinfo top get numframes] set complex [atomselect top "protein and noh"] set sel [atomselect top "protein and noh"] set sasa [measure sasa 1.40 $complex -restrict] for { set i 0 } { $i < $nf } { incr i } {     $sel frame $i puts $fp "$i $sasa" } close $fp However, the output file gives the same value for all frames: 0 21724.5625 1 21724.5625 2 21724.5625 3 21724.5625 ... 1250 21724.5625 I think the calculation for the first frame was repeated to all others. I am not expert in TCL language, so I appreciate very much if an experienced user could tell me what is wrong with the script. Thanks in advance Flavio