VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Feb 02 2020 - 11:19:46 CST

Actually, we always encourage people to keep discussions on the mailing
list (unless they get very deep into one specific technical issue), so that
they can serve as a searchable resource in the future. This is why the
vmd-l archive is such a powerful starting point for vmd-related problems
(the same goes for any publicly archived mailing list). I would highly
recommend filtering vmd-l messages to a separate division of your inbox, or
subscribing to the mailing list digest (see
https://www.ks.uiuc.edu/Research/vmd/mailing_list/), if you don't want to
see all messages.
Best,
Peter

On Sun, Feb 2, 2020 at 11:35 AM soodabeh ghaffari <
soodabehghaffari_at_gmail.com> wrote:

> Can I ask you to remove me from your discussion?
>
> On Sun, Feb 2, 2020 at 11:34 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> 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
>>>>
>>>>