Re: Automatic PSF Builder Problem

From: ehenriques_at_qui.uc.pt
Date: Sat Mar 12 2011 - 10:49:05 CST

Hi,

Try editing the chain

P1 8 1- 65 PROP CTER Prot

in AutoPSF graphical interface and replace the CTER ending by the one
you want, which in your case is ACP (ACE for proline).

Hope it helps,

E.

Citando Marc Charendoff <mcharend_at_sbcglobal.net>:

> Hello,
>
> 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
> error
>
> 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
> "::autopsf::makepatches_gui"
> 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

-- 
Elsa S. Henriques                     e-mail: ehenriques_at_qui.uc.pt
Investigadora Auxiliar
Biologia Estrutural e Computacional (@CNC)
e Grupo de Química Estrutural (@CCC)
B.25 - Laboratório RMN
Departamento de Química - Universidade de Coimbra
3004-535 COIMBRA                         Portugal
Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

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