[gmx-users] Re: resolved pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Sat Oct 2 15:44:23 CEST 2010

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.

See comments inline below.

ahmet yıldırım wrote:
> Hi,
> You said "Per the instructions I sent before, you need to either add the 
> location of your Gromacs installation to your PATH (in whatever shell 
> configuration file, likely .bashrc) or source GMXRC every time you log 
> in to a new terminal.  Once your Gromacs installation is recognized by 
> your shell environment you can run all the commands."

Yes, so have you followed that advice?  You've given no indication that you have.

> I have 1.pdb file. I want to convert 1.gro and 1.top this file using 
> pdb2gmx command.
> *pdb2gmx –f 1.pdb –o 1.gro –p 1.top*

That's the proper command, provided that the subdirectory containing pdb2gmx is 
in your PATH, which you can accomplish by doing either of the two things I have 
told you to do.

> Can you give an example?
> ab at ab-desktop:~/usr/bin$ .............?????

Sorry, I don't understand what you're asking for here.


> Please, don't be angry with me.I am a Ph.D. student, Department of 
> Physics, Siirt University, Turkey.
> Thanks in advance
> -- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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