[gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs

[David van der Spoel]

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
> 
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-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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