VMD-L Mailing List

From: Stanley, Yemin Shi (shi_yemin_at_yahoo.com)
Date: Sat Jan 27 2007 - 21:55:02 CST

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