From: Gordon Wells (gordon.wells_at_gmail.com)
Date: Wed Jan 23 2013 - 14:44:41 CST
(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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