[gmx-users] Re: .mdp format

[Justin A. Lemkul]

Chih-Ying Lin wrote:

> Hi
> if I am in my working directory,
> and give the command in my .mdp file
>
> include           =-I/my_working_directory
>
>
> I will get the following error....
> Program grompp, VERSION 3.3.3
> Source code file: grompp.c, line: 469
> Fatal error:
> number of coordinates in coordinate file (xxx.gro, 24)
>              does not match topology (xxx.top, 0)
>
>
>   

When you get error messages, the first step should be to do a thorough 
search of the wiki (wiki.gromacs.org) and the mailing list archive.  If 
you had done this, you would have come across:

http://wiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

> With Justin explaination,
> More or less, yes.  By default, Gromacs searches $GMXLIB and the current
> working directory for the necessary topology information.  The "include
> = -I" line can be used to specify the location(s) of other necessary
> topologies.
>
> Does it mean that I could simply delete the
> "include=-I/my_working_directory" command??
>
>   

Yes, including the working directory would be redundant.

-Justin

> Thanks a lot
>
> Lin
>
>   

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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