Re: [gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs
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 listgmx-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 listgmx-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
[gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs
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? Thanks for help. ___ gmx-users mailing listgmx-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
Re: [gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs
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! :-) Mark ___ gmx-users mailing listgmx-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
Re: [gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs
it seems there's a problem with my compiler. I succesfully run grompp in another computer with gromacs distribution. I compare and check the two ggc version. On Nov 9, 2007 7:10 PM, Mark Abraham [EMAIL PROTECTED] 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! :-) Mark ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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
