Re: Autopsf error with a modified top file

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Feb 18 2009 - 15:24:59 CST

Hi Vlad,
could you send me the last few lines of output in your console? Usually
whatever error was encountered will be clearer based on that.
Best,
Peter

CHINDEA Vlad wrote:
> Hi everybody
>
> I am trying to parametrize some drug molecules for NAMD simulations.
> As a first approximation I patched as much information as possible,
> regarding atom types and charges, from the existing topology files
> with some additional charge input for QM calculations. The plan is to
> compare the MD simulated structure with the X-ray resolved one in
> order to identify areas for further improvement. I generated the
> attached "raw and abreviated" top file but when I try to use it
> with Autopsf in order to prepare the input for the MD I get the
> following error message, at "Create chain" step:
>
> /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 29)
> invoked from within
> "psfsegments $logfileout"
> (procedure "::autopsf::afterchains_gui" line 50)
> 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 24)
> invoked from within
> "tk::ButtonUp .autopsf.chains.finish
> "
> (command bound to event) /
>
> Is there something wrong with my top file ? Maybe I chopped it a
> little too much...!?
>
> Many thanks for your support
>
> Vlad Chindea
>
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