VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Feb 02 2020 - 09:53:28 CST

Hi Peter
thanks for the offer of help. As it is a huge system, I want to analyze it
again, sending files if I continue to be in the dark

kind regards
francesco

On Sun, Feb 2, 2020 at 3:01 PM Peter Freddolino <petefred_at_umich.edu> wrote:

> 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
>>
>>