[gmx-users] cannot generate .top file

[Mark Abraham]

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... 
http://www.control-escape.com/linux/lx-postinstall.html#user

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 
http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation

> 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!

Mark