VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 10 2015 - 11:34:05 CST

I would suggest that you consider upgrading to a newer version of VMD
that includes the nanotube plugin, as it may make your life
easier by (hopefuly rapidly) getting you past the issues you've run into.
Is there some particular reason you're still using such an old version
of VMD?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 09, 2015 at 06:50:37PM +0000, zeynab hoseyni wrote:
> Hi Axel,
> Thanks for your answer and sorry to reply with delay. I was traveling
> around and couldn't answer earlier..
> Well the point is that in the vmd version (1.9) I have installed on my
> laptop
> there isA nano-tubeA plugin and it is easy to make the needed pdb in this
> way
> but to make the psf file, it isn't so much straight forward.A I searched
> in in vmd
> mailing list and found the following script that uses topotools to make
> the psf
> file after loading the pdb file:
> package require topotools
> topo retypebonds
> topo guessangles
> topo guessdihedrals
> mol reanalyze 0
> animate write psf cnt.psf
> I used this script and made the cnt.psf with no problem, but as soon as I
> start
> simulation of nanotube, using namd, I face with this error:
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR C C C (ATOMS 1 2 5)
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR C C C (ATOMS 1 2
> 5)
> It seems still something is wrong and there isn't enough match between psf
> file
> and parameter file (I used par_all27_prot_lipid.inp for parameter file of
> namd).
> But when I use theA make_arm.tcl script everything is alright and the
> simulation
> goes well.. Could you guide me on this?
> Thanks,
> ZeynabA
> On Mon, Dec 7, 2015 at 1:03 PM, Axel Kohlmeyer <[1]akohlmey_at_gmail.com>
> wrote:
>
> On Sun, Dec 6, 2015 at 8:39 AM, zeynab hoseyni <[2]zmhoseyni_at_gmail.com>
> wrote:
> >
> > ---------- Forwarded message ----------
> > From: zeynab hoseyni <[3]zmhoseyni_at_gmail.com>
> > Date: Sun, Dec 6, 2015 at 1:39 PM
> > Subject: Re: vmd-l: couldn't execute "psfgen": no such file or
> directory
> > To: Axel Kohlmeyer <[4]akohlmey_at_gmail.com>
> >
> >
> > Hi Axel,
> >
> > Thanks for your answer. I've found the psfgen binary file from the
> > namd installation files I already downloaded and put it in the same
> > directory as that of the make_arm.tcl script. I performed it again:
> > sourcing and running the mentioned command within tk console
> > but still receiving the same error..
> > Do you have any idea what is wrong?
>
> this is just normal behavior on any unix-like operating system. the
> current working directory is not part of the search path for
> executables (and for good reasons. it is a bad security problem to
> have the current working directory have precedence over the PATH
> environment).
>
> you have to use an absolute path or adjust your PATH environment
> variable. i would expect that the tutorial you are following contains
> instructions for that. i suggest you re-read the docs.
>
> also, is there a specific reason that you use these (old) scripts and
> not the (newer) nanotube plugin in VMD?
>
> axel.
>
> > All the Best,
> > Zeynab
> >
>
> --
> Dr. Axel KohlmeyerA [5]akohlmey_at_gmail.comA [6]http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
> References
>
> Visible links
> 1. mailto:akohlmey_at_gmail.com
> 2. mailto:zmhoseyni_at_gmail.com
> 3. mailto:zmhoseyni_at_gmail.com
> 4. mailto:akohlmey_at_gmail.com
> 5. mailto:akohlmey_at_gmail.com
> 6. http://goo.gl/1wk0 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/