• ## Outreach

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Thu Sep 03 2009 - 07:45:06 CDT

Dear VMD users:

I was using script below to calculte a matrix that contains rmsd between structures from a dcd file:

set outfile [open rmsd_min.txt w];

set sel1 [atomselect top "protein and backbone and noh"]

set nf1 [molinfo top get numframes]

set sel2 [atomselect top "protein and backbone and noh"]

for {set i 0 } {\$i < \$nf1 } { incr i } {

for {set j \$i } {\$j < \$nf1 } { incr j } {

\$sel1 frame \$i

\$sel2 frame \$j

\$sel2 move [measure fit \$sel2 \$sel1]

set rmsd_matrix(\$i,\$j) [measure rmsd \$sel2 \$sel1]

\$sel2 move [measure fit \$sel2 \$sel1]

set rmsd_matrix(\$j,\$i) [measure rmsd \$sel2 \$sel1]

}}

for { set i 0 } { \$i < \$nf1 } { incr i} {

for { set j 0 } { \$j < \$nf1 } { incr j } {

puts -nonewline \$outfile "\$rmsd_matrix(\$j,\$i) "

}

puts \$outfile ""

}

close \$outfile

It was working well. I created a mutated structure and now I need to calculate RMSD matrix between structures from both dcd files (one of native structure and another from mutated structure), and I do not know how I should change the script above to do it. I wait somebody can help me.

King regards

Andres

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