VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Oct 13 2020 - 18:40:42 CDT

Hi Yuvam,
To start off, could you please send your input structure and the
intermediate files that are produced by aufopsf? It is also important to
specify exactly what steps you took in each stage of the GUI leading up to
the error.
Best,
Peter

On Sat, Oct 10, 2020 at 5:51 AM Yuvam Bhateja <yuvamb16_at_gmail.com> wrote:

> Greetings experts,
>
> I am trying to solvate my silver nanoparticle using VMD.
> I have created the pdb file for NP but whenever I try to create psf file
> using "Automatic psf builder", it gives 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 24)*
> * invoked from within*
> *"tk::ButtonUp . autopsf.chains.finish"*
> * (command bound to event)*
>
> I got the make error when creating a psf file for FMN molecule consisting
> of 32 atoms only.
>
> Can anyone please suggest how to overcome this problem?
>
> Regards
> Yuvam Bhateja
>
>