From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 02 2010 - 18:11:00 CDT
On Wed, Jun 2, 2010 at 6:37 PM, Leonardo Herrera <ldhz04_at_yahoo.com.mx> wrote:
> Hi somebody
> Can anybody help me?
> I added a harminic restraint on two atoms three times in one tclforcesscript in my protein during simulation. But I have an error when I am running my simulation. the error is:
>
>
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: wrong # args
> while executing
> "et retval {}"
this looks like a typo. probably you want to do "set retval {}"
> (procedure "vecnorm" line 7)
> invoked from within
> "vecnorm $r12"
> (procedure "calcforces" line 13)
> invoked from within
> "calcforces"
>
> Charm++ fatal error:
> FATAL ERROR: wrong # args
> while executing
> "et retval {}"
> (procedure "vecnorm" line 7)
> invoked from within
> "vecnorm $r12"
> (procedure "calcforces" line 13)
> invoked from within
> "calcforces"
>
> and my tclscript is
>
> set k 100.00
> set r0 2.15
>
> set count 0
>
> set atoms1($count) 983
> set atoms2($count) 9232
>
> incr count
>
> set atoms1($count) 1626
> set atoms2($count) 9232
>
> incr count
>
> set atoms1($count) 6794
> set atoms2($count) 9232
>
> incr count
>
> for {set i 0} {$i < $count} {incr i} {
>
> addatom $atoms1($i)
> addatom $atoms2($i)
> }
>
> print "tclfprces action"
>
> proc calcforces {} {
>
> global k r0 atoms1 atoms2 count
>
> loadcoords p
>
> for {set j 0} {$j < $count} {incr j} {
>
> set r12 [vecsub $p($atoms1($j)) $p($atoms2($j))]
>
> set r [veclength $r12]
>
> set n0 [vecnorm $r12]
>
> set force [expr $k*($r-$r0)]
>
> set f1 [vecscale $force $n0]
>
> set f2 [vecscale -$force $n0]
>
> addforce $atoms1($j) $f1
> addforce $atoms2($j) $f2
> }
> }
>
>
> # Ther is a definition of subroutine veclenght and vecnorm
> # Returns: the vector length
>
> proc veclength {v} {
> set retval 0
> foreach term $v {
> set retval [expr $retval + $term * $term ]
> }
> return [expr sqrt($retval)]
> }
>
> # Returns: the normal vector
> proc vecnorm {v} {
> set sum 0
> foreach term $v {
> set sum [expr $sum + $term*$term]
> }
> set sum [expr sqrt($sum)]
> et retval {}
^^^^^^^^^^^^^^^^^^^
and here it is.
cheers,
axel.
> foreach term $v {
> lappend retval [expr $term / $sum]
> }
> return $retval
> }
>
> thanks in advance
>
> MenB Leonardo David Herrera Zúñiga POSGRADO EN QUÍMICA UAMI Biofisicoquímica Universidad Autonoma Metropolitana IztapalapaTel. +52 (55) 5804 4674 ldhz04_at_yahoo.com.mx
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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