Automatic PSF Builder Problem

From: Marc Charendoff (
Date: Fri Mar 11 2011 - 10:43:15 CST


       Sorry for bugging again, but I'm trying to better describe an issue with
ACE capping an N-terminal proline. When I use AutoPSF I do the following :

Step 1: identify the input and output file basenames and let program use the
default topology files

Step 2: Check Protein, and allow the program to Guess and split chains (I have
only a small eight amino acid peptide)

Step 3: Observe the Chains identified: P1 8 1- 65 PROP
 CTER Prot

Step 4: Add patches ACE P1:1 and CT2 P1:8 (as I wish to cap my
terminal peptides)

When I hit the apply patches and finish PSF/PDBs though, I get the following

can't read "logfileout": no such variable
can't read "logfileout": no such variable
    while executing
"puts $logfileout "Applying patch: [lindex $patch 0] [lindex $patch 1]:[lindex
$patch 2]""
    (procedure "::autopsf::makepatches_gui" line 15)
    invoked from within
    invoked from within
".autopsf.patches.finish invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 23)
    invoked from within
"tk::ButtonUp .autopsf.patches.finish"
    (command bound to event)

Guidance appreciated. Thanks, Marc

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