Re: error in scripting

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 16 2009 - 07:36:50 CST

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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.

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