Mark Abraham wrote:
I installed ffamber ports for gromacs, generated gro and topology
files for a DNA structure with pdb2gmx, a box with editconf and added
solvation with genbox. When I try to run grompp i obtain these errors:
checking input for internal consistency...
calling cpp -traditional...
processing topology...
Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
ERROR 0 [file "gr_Nast.top", line 761]:
No default Bond types
ERROR 0 [file "gr_Nast.top", line 3352]:
No default Angle types
ERROR 0 [file "gr_Nast.top", line 3354]:
No default Angle types
It seems gromacs don't read ffamber* force field information, however
i using the directive
include = -I\home\jantonioms\Programs\gromacs\share\gromacs\top
in *.mdp file
Can anyone have an idea?
I don't know if it is the cause of the problem, but backslashes are not
usually interpreted as directory & file separators on Unix - unlike
Windows. Use forward slashes. As a first guess, I'd say that cpp is
interpreting your include directive with the backslashes starting escape
sequences for funky meanings, hence failing to find ffamber. That assumes
you've put ffamber in that location, of course! :-)
A simple workaround is to put the amber files in your working directory.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
