VMD-L Mailing List

From: Al-Ali, Hassan (HAlAli_at_med.miami.edu)
Date: Tue Oct 05 2010 - 22:49:34 CDT

Hello,

I have two questions:

1- I need to run NAMD on a model which contains a peptide chain with a K-linked ubiquitin. Is there a topology file/patch for the Ub-Cterm-NZ-lysine peptide bond?

2- I am trying to cap the N-termini with ACE, as they are not true N-termini. I used the top_all22_prot topology file and VMD autoPSF module. However, I keep getting this message:

ERROR: failed to apply patch
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
ERROR: failed to apply patch
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
    while executing
"patch ACE P3:1"
    ("eval" body line 1)
    invoked from within
"eval "patch [lindex $patch 0] [lindex $patch 1]:[lindex $patch 2]""
    (procedure "::autopsf::makepatches_gui" line 17)
    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 24)
    invoked from within
"tk::ButtonUp .autopsf.patches.finish"
    (command bound to event)

Thanks in advance,
Hassan