Re: error in scripting

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 25 2009 - 01:08:21 CST

On Wed, 2009-11-25 at 11:38 +0530, ipsita basu wrote:
> Please reply me. I have sent you many mails but I receive no mail from
> you for a long time. But I really need your help as there are no one
> in mmy lab who knows namd. I can't proceed further without your help.
> So please help.

as i told you before, you have to debug your .psf file.
whether is runs with CHARMM is irrelevant. you have to
keep in mind, that MD calculations often "work" with
bogus inputs and some errors only show up by chance.

even if you post the same question another five times,
your chances of getting somebody to do this debugging
for you are miniscule.

even though it does not fully apply, have a look at:
http://catb.org/~esr/faqs/smart-questions.html

the consequence is the following: if you are convinced
that NAMD is at fault, then you have to make a convincing
argument for it. "it doesn't work" or "it runs with charmm"
is not. if you or your colleagues don't know enough about
NAMD, then - again - it is not the fault of the people here
and all you can do is to learn more about it. for that purpose,
i recommend training with small problems that are easy to
debug and systematically trying to improve your understanding
of the whole process of running MD simulations.

the fact that you feel you cannot proceed is tough on you,
but everybody has been in that situation before and nobody
here gets paid for helping other people, let alone doing
what is ultimately your work for you. this may sound harsh
right now, but how much would _you_ do for somebody asking
you about something that is not a concern for you?

cheers,
   axel.

> On 11/20/09, ipsita basu <ibasu788_at_gmail.com> wrote:
>
>
> ---------- 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
>
>
>
> --
> 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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