[gmx-users] nucleic acis simulation

Miguel Ortiz Lombardia molatwork at yahoo.es
Tue Feb 28 12:50:43 CET 2006

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David van der Spoel escribió el 28/02/06 11:25 :
> Miguel Ortiz Lombardia wrote:
> Thank you Maik.
> The AMBER ports are some I'm testing, sure.
> BTW, I can't get it ready if I solvate the model. Everything goes fine
> until grompp complains:
> $> grompp -v -f em -c watered -o em -p nucT
> (...)
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 1108
> Fatal error:
> [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
>              Atom index (1) in settles out of bounds (1-0)
> -------------------------------------------------------
> Any clues of what may be wrong?
>> order of bits in the topology file. chpater 5

The order of the elements in the topology file seem the same whether
this is created using ffG43a1 or ffamber99. However, only the second
prompts the error at the grompp step. I read the topology and
molecule.itp file formats in chapter 5 of the manual (v. 3.2), but I was
not able to spot the problem. Could you please be more precise?

Thank you!

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: molatwork at yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
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Je pousse en liberté
Dans les jardins mal fréquentés!
                                                       Georges Brassens
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