Re: error in scripting

From: ipsita basu (ibasu788_at_gmail.com)
Date: Wed Nov 25 2009 - 00:08:04 CST

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.

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

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