VMD-L Mailing List
From: Stanley, Yemin Shi (shi_yemin_at_yahoo.com)
Date: Sat Jan 27 2007 - 21:55:02 CST
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Hi,
I got a error message when generate psf from pdb. Could anybody kindly pls help?
(WinVMD, Autopsf)
The step outline is:
1) Load the molecule
2) Extentions->modelling->automatic psf builder
3) all parameter are set to default in the auto psf dialog box.
Once I click the "I'm feeling lucky" button, it comes out the following messeger:
==================================================
Autopsf has detected on unparameterized components:
Don't worry, there are several things you can do:
1) Load additional topology file that contains missing information and rerun psfgen.
2) Delete the component from your system and rerun psfgen.
3) Parameterize the unknown component using Paratool.
----------------------------------------
Zn 1 Atoms ZINC ION
----------------------------------------
Once I click the parameterize button, it comes out the following error message:
-------------------------------
atomsel : setbondorderss: Need one bond order list for each selected atom
atomsel : setbondorderss: Need one bond order list for each selected atom
while executing
"$atom0 setbondorders [list $bondorder0]"
(procedure "import_bondorders_from_topology" line 84)
invoked from within
"import_bondorders_from_topology $molidparent"
(procedure "::Paratool::paratool" line 103)
invoked from within
"::Paratool::paratool -top $topfiles -parentid $tmpmolid -unparsel $sel -basemol ${basename}_${resname}_${i}.xbgf -extrabonds $extrabonds"
(in namespace inscope "::autopsf" script line 20)
invoked from within
"::namespace inscope ::autopsf {
variable unparsel
set i [.fchooser.frag.topo.list.list curselection]
set frag [lindex $unparsel $i]
..."
invoked from within
".fchooser.frag.topo.buttons.add invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 24)
invoked from within
"tk::ButtonUp .fchooser.frag.topo.buttons.add
"
(command bound to event)
-------------------------------
Thanks for help
Rgds
Stanley
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