From: ipsita basu (ibasu788_at_gmail.com)
Date: Thu Nov 19 2009 - 23:33:25 CST
---------- Forwarded message ----------
From: ipsita basu <ibasu788_at_gmail.com>
Date: Nov 17, 2009 11:12 AM
Subject: Re: namd-l: error in scripting
To: Axel Kohlmeyer <akohlmey_at_gmail.com>
But I and my labmembers did many jobs in charmm with this topology and
parameters file and I made the psf file from crd file using charmm. While
writing the psf file I use this command: write psf card xplor unit 11
Is there any problem during writing the psf file? Otherwise this is
difficult to change the psf file. I have sent you this before but get no
reply. But I really need help. Otherwise I can't proceed. So please help.
On 11/16/09, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> On Mon, Nov 16, 2009 at 1:47 AM, ipsita basu <ibasu788_at_gmail.com> wrote:
> > Dear all,
>
> [...]
>
>
> > Warning: Ignored 4020 bonds with zero force constants.
> > Warning: Will get H-H distance in rigid H2O from H-O-H angle.
> > FATAL ERROR: Atom 70 has bad group size. Check for duplicate bonds.
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: Atom 70 has bad group size. Check for duplicate
> bonds.
>
>
> [...]
>
>
> > Aborted
> > Please help me. What is the solution of this problem? I am very new to
> namd.
> > I really need your help.
>
>
> well, the error message even gives you a hint. what else do you want?
> so check your topology (.psf) file. it seems to have some bad, incorrect
> or bogus structure data in it.
>
> cheers,
> axel.
>
> >
> > --
>
> > Ipsita Basu
> > Research Fellow
> > c/o : Dr. Chaitali Mukhopadhyay
> > Rajabazar Science College
> > 92 APC Road
> > Kolkata - 700009
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
-- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 700009 -- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 700009
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