VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Feb 02 2020 - 08:04:37 CST

Hi Francesco,
This seems odd. Can you send a pdb file that reproduces this behavior, and
exact instructions on how you tried running autopsf?
Thanks,
Peter

On Sat, Feb 1, 2020 at 6:19 PM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Hello
> From AutoPSF with a RNA-protein assembly (cut to a sphere of 60A radius) I
> got the following vecsub error
>
> vecsub: two vectors don't have the same size
> vecsub: two vectors don't have the same size
> while executing
> "vecsub $x $y"
> (procedure "vecdist" line 2)
> invoked from within
> "vecdist $Ccoords $Ncoords"
> (procedure "split_protein_and_water_pdb" line 250)
> invoked from within
> "split_protein_and_water_pdb "${basename}-temp.pdb""
> (procedure "::autopsf::aftersels_gui" line 55)
> invoked from within
> "::autopsf::aftersels_gui"
> invoked from within
> ".autopsf.sels.next invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autopsf.sels.next"
> (command bound to event)
>
> Jmol does not find errors.
> Which kind of error should I look for in the starting pdb file?
> Nonmatching ID?(huge
>
> Thanks for any suggestion
> francesco pietra
>
>