From: Francesco Pietra (
Date: Mon Feb 03 2020 - 03:32:49 CST

Hi Peter
It is probably a trivial affair, though not yet fully resolved. The vecsub
problem arose with the sphere60.pdb removed of osmiumhexamino (needed for
Xray diffr), as well as RNA and proteins of less than a certain number of
residues (which had worked well with sphere20.pdb for the same system). It
can be reproduced for the same curtailed system, however, I have not yet
rebuilt the curtailed system from scratch.

With sphere60.pdb only cleaned from osmiumhexamino, AutoPSF has no problems
and the system can be minimized without restraints and heated, for the
moment with some restraints, without problems. It is only very expensive at
the cluster.

best regards

On Sun, Feb 2, 2020 at 3:01 PM Peter Freddolino <> 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 <>
> 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
>> " invoke"
>> ("uplevel" body line 1)
>> invoked from within
>> "uplevel #0 [list $w invoke]"
>> (procedure "tk::ButtonUp" line 22)
>> invoked from within
>> "tk::ButtonUp"
>> (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