From: Gordon Wells (gordon.wells_at_gmail.com)
Date: Wed Jan 23 2013 - 17:18:46 CST
I get this when trying to mutate a protein and produce the fep files. I
tried this for different proteins and different builds of vmd (on mac and
linux).
PS, forgot to mention that changes I posted are for the file mutator.tcl in
the $VMDDIR/plugins/LINUXAMD64/tcl/mutator1.4 directory
The script seems to iterate over each protein segment but this means it
tries to generate the hybrid amino acid code each time. I put the condition
in to stop this.
-- max(∫(εὐδαιμονία)dt)
Dr Gordon Wells
Chemistry Department
Emory University
Atlanta, Georgia, USA
On 23 January 2013 17:45, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Can you explain what you do to generate the error in the first place?
>
> On Jan 23, 2013, at 3:44 PM, Gordon Wells wrote:
>
> (apologies, forgot to post to the list)
>
> I've been having similar problems with the mutator plugin, it crashes when
> trying to generate FEP input files. This is the error:
>
> can't read "aa()": no such element in array
> ERROR: failed while building segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
>
> this seems to fix it, "diff before after":
> < set hyb [format "%s2%s" $aa($oldres) $aa([string toupper
> $mut])]
> < if { [info exists cmdline(-ressegname)] } {
> < #puts "\n Mutator DEBUG: $i $ressegname"
> < if { $i == $ressegname } {
> < puts "\n Mutator: Residue $oldres $resid of
> segment $ressegname is now $hyb"
> < mutate $resid $hyb
> < }
> < } else {
> < puts "\n Mutator: Residue $oldres $resid of segment $i
> is now $hyb"
> < mutate $resid $hyb
> < }
> ---
> > puts $oldres
> > puts $mut
> > if {[$alpha num] == 1} {
> > set hyb [format "%s2%s" $aa($oldres) $aa([string
> toupper $mut])]
> >
> > if { [info exists cmdline(-ressegname)] } {
> > #puts "\n Mutator DEBUG: $i $ressegname"
> > if { $i == $ressegname } {
> > puts "\n Mutator: Residue $oldres $resid of segment
> $ressegname is now $hyb"
> > mutate $resid $hyb
> > }
> > } else {
> > puts "\n Mutator: Residue $oldres $resid of segment $i is
> now $hyb"
> > mutate $resid $hyb
> > }
> >
> > }
> >
>
>
>
> -- max(∫(εὐδαιμονία)dt)
>
> Dr Gordon Wells
> Chemistry Department
> Emory University
> Atlanta, Georgia, USA
>
>
> On 23 January 2013 12:29, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>
>> No idea.
>>
>> If the mutator plugin breaks, it should be fixed. Send me off-list the
>> files (if they aren't too big) and an exact description of what you tried
>> that crashed it.
>>
>>
>> On Jan 23, 2013, at 12:21 PM, Thomas Albers wrote:
>>
>> > Hello!
>> >
>> > On Wed, Jan 23, 2013 at 12:16 PM, JC Gumbart <gumbart_at_ks.uiuc.edu>
>> wrote:
>> >> I have no idea what you're trying to do here, but it looks very
>> non-standard. Try using the Mutator plugin in VMD on your original
>> structure (with the FEP box checked) to produce the files you need.
>> >
>> > But it works. :-) The Mutator plugin actually has its own problems,
>> > when I was using it to mutate the glycine molecule that sits in the
>> > binding pocket the plugin always crashed.
>> >
>> > Anyway, I downloaded the NAMD-2.9-Linux-x86_64-ibverbs binary, and
>> > that one works fine on our cluster. The one that we compiled
>> > ourselves does not. Would you have any hunch what went wrong during
>> > compilation.
>> >
>> > Regards,
>> > Thomas
>>
>>
>>
>
>
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