VMD-L Mailing List

From: Aishwarya Smriti (smritiaishwarya85_at_gmail.com)
Date: Mon Sep 18 2017 - 10:23:36 CDT

Thank You. I'll try it that way.

On Mon, Sep 18, 2017 at 8:48 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> I'm pretty sure that plugin was not developed/tested for special
> structures
> like those produced by the carbon nanotube builder plugin that may need
> special, or additional topology or parameter files. It was intended to
> be used for straightforward PDB structures. You will probably be better
> off to use psfgen or topotools yourself to combine the carbon nanotube with
> your protein(s).
>
> I'll see about looking at what the code is doing there and
> making changes to the documentation to indicate this if the issues
> I'm expecting are what is causing this error.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Sep 17, 2017 at 02:35:44PM +0530, Aishwarya Smriti wrote:
> > Hi!
> >
> > I created a CNT using Nanotube builder plug-in of VMD (version 1.9.3)
> of
> > dimension (5,10). I created pdb and pdf files by typingÂ
> > set x [atomselect 0 "all"]
> > $x writepdb cnt.pdb
> > $x writepsf cnt.psf
> >
> > The psf and pdb files were successfully created. I wanted to merge
> this
> > with a protein file, so I used Merge Structures plug in to which I
> got an
> > error message as shown below:
> >
> > MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over--001a113ad434967dea0559785308--