VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed May 01 2019 - 13:24:31 CDT

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