VMD-L Mailing List

From: Yuvam Bhateja (yuvamb16_at_gmail.com)
Date: Sat Oct 10 2020 - 03:04:41 CDT

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