VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed May 01 2019 - 21:26:03 CDT

That does seem odd. Out of curiosity, what happens if you try the same
thing in a clean directory starting in a fresh vmd session?
Also, do you have the _autopsf.log file from the successful vs.
unsuccessful runs?

Thanks,
Peter

On Wed, May 1, 2019 at 5:56 PM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Hi Peter
> During the auto-procedure I took notice of the segments which were created
> and the suffix added 5TER 3TER (for RNA), NTER CTER (for the proteins), and
> NONE NONE for Mg++. All looked out to be correct, but I understand that
> some error escaped my attention. It is curious anyway that a few days ago
> psf/pdb was correctly created with the same files. Even now, the temp.pdb
> files for the various segments are correct. It is only the last step that
> encounters problems
> thanks
> francesco
>
>
> On Wed, May 1, 2019 at 9:51 PM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Hi Francesco,
>> I think your comment at the bottom may provide a clue. When you say "there
>> is none explicitly because proteins and RNA have been cut within a sphere
>> without any further action", does that mean that you have a bunch of
>> disjoint protein chains being used as input to autopsf? If so, then what
>> autopsf will try to do by default is turn each one into a chemically
>> correct polypeptide chain, which includes adding appropriate terminal
>> groups. If this is not the desired behavior, you need to specify it by
>> manually editing the set of chains shown in "Chains Identified" box. (but I
>> have to ask at this point, what *do* you want it to do with the ends of
>> your selected region?)
>> Best,
>> Peter
>>
>> On Wed, May 1, 2019 at 3:47 PM Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>>> Hi
>>> After a long time I am back at autopsfgen (1.9.4a12 VMD) because with so
>>> many Mg++, proteins and RNA segments the psfgen/vmd_text procedure, which I
>>> normally use, would be too laborious.
>>> Autopsfgen worked well for me a few days ago, giving correct psf/pdb,
>>> now no more. The error
>>>
>>> ERROR: failed on end of segment
>>>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>>>> ERROR: failed on end of segment
>>>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>>>> while executing
>>>> "segment $segid {
>>>> pdb $segfile
>>>>
>>>> # We alias the C-terminal OXT atoms to OT2 so that psfgen has to
>>>> guess one atom less.
>>>> # Otherwise psf..."
>>>> (procedure "psfsegments" line 37)
>>>> invoked from within
>>>> "psfsegments $logfileout"
>>>> (procedure "::autopsf::afterchains_gui" line 66)
>>>> invoked from within
>>>> "::autopsf::afterchains_gui"
>>>> invoked from within
>>>> ".autopsf.chains.finish invoke"
>>>> ("uplevel" body line 1)
>>>> invoked from within
>>>> "uplevel #0 [list $w invoke]"
>>>> (procedure "tk::ButtonUp" line 22)
>>>> invoked from within
>>>> "tk::ButtonUp .autopsf.chains.finish"
>>>> (command bound to event)
>>>>
>>>
>>> is unclear to me. As to OXT, there is none explicitly because proteins
>>> and RNA have been cut within a sphere without any further action
>>>
>>> Is that a way for a more verbose output?
>>>
>>> thanks
>>> francesco pietra
>>>
>>