Miguel Ortiz Lombardia wrote:
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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
- --
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: [EMAIL PROTECTED]
www: http://www.ysbl.york.ac.uk/~mol/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!
Georges Brassens
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the position in the top file where the spc.itp was included is wrong.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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