VMD-L Mailing List

From: zeynab hoseyni (zmhoseyni_at_gmail.com)
Date: Wed Dec 09 2015 - 12:50:37 CST

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 is nano-tube 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. 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 the make_arm.tcl script everything is alright and the
simulation
goes well.. Could you guide me on this?

Thanks,
Zeynab

On Mon, Dec 7, 2015 at 1:03 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sun, Dec 6, 2015 at 8:39 AM, zeynab hoseyni <zmhoseyni_at_gmail.com>
> wrote:
> >
> > ---------- Forwarded message ----------
> > From: zeynab hoseyni <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 <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 Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>