AMBER Archive (2007)

Subject: Re: AMBER: antechamber

From: Barbault Florent (florent.barbault_at_paris7.jussieu.fr)
Date: Mon Jul 09 2007 - 09:59:03 CDT

Hi,

If it is a classical DNA strand, antechamber is not suitable. You may have to
read directly your mol2 file or pdb file with leap or xleap. I think you have
to use leaprc.ff03 for dna.
Regards
Florent Barbault

Le lundi 9 juillet 2007, Marie Brut a écrit :
> I prepared a mol2 file containing the coordinates of a small double strand
> of DNA. Then, I used antechamber to generate a prepin file but here is the
> problem
>
> : until the end of the first strand, everything is normal, but after the
> : prepin
>
> file is like this :
>
> 67 X 0.000000 0.000000 0.000000
> 68 X 0.000000 0.000000 0.000000
> ....
>
> Could anyone help me to solve my problem ?
>
> Thanks,
> Marie
>
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-- 
----------------------------------------------------------
Dr Florent Barbault
Maitre de conferences
Universite Paris VII
Laboratoire ITODYS
1, rue Guy de la Brosse
75005 Paris FRANCE
http://perso.wanadoo.fr/barbault
tel  : (33) 01-44-27-68-21
mail : florent.barbault_at_paris7.jussieu.fr
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