VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed May 01 2019 - 16:56:22 CDT

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
>>
>