[gmx-users] cannot generate .top file

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 29 07:01:55 CET 2008

Kwee Hong wrote:
> Oo.. I'm so sorry for I'm not aware of this. But I'm really new to linux 
> environment and don't really have a good mastering skill on the 
> commandline that it works with. As you said that I'm not given the 
> permission to write in that directory, sudo was the only thing that I 
> can think of out from my knowledge. I don't really know how to do my 
> work at the subdirectory of my hoe directory. 

OK. Just to prove I'm not an ornery old crank, here's a URL pointing out 
just some of the pitfalls of working as superuser... 

In UNIX as in any field, the "Good Things To Do" are written in the 
blood and time of people who thought the above didn't apply to them! :-)

> And does the meaning of 
> "adjust your environment variables to give you ready access to GROMACS 
> stuff by using "source /path/to/GMXRC" using the  path in which you 
> installed the GROMACS binaries" requires me to make some changes in the 
> source code or just by typing "source /path/to/GMXRC" at the terminal 
> would have open the access for me in the directory? 

The latter. See 

> I'm sorry for my ignorance... I think I would better get some books on 
> linux environment and read on it first.

Great idea. Start with a web search - there's heaps of free UNIX 
tutorial material. Also, do some GROMACS tutorial material you can find 
on the web. These will give you more of a handle on how GROMACS things 
get done.

Good luck!


More information about the gromacs.org_gmx-users mailing list