[gmx-users] selecting res CYS from G53a5 using pdb2gmx

Justin Lemkul jalemkul at vt.edu
Wed Jan 9 02:13:11 CET 2013

On 1/8/13 8:05 PM, Payman Pirzadeh wrote:
> Since gromacs is globally installed on the cluster, I am making local
> modifications. What was strange was I modified the three files, and I ran
> pdb2gmx with them, and it failed (it could not find certain atoms?!). Then I
> copied the whole gromos53a5 folder to my working directory and moved these
> files into it, and I used the -ff option, but it still opened the global
> folder. So, I kept the three modified files in my working directory + the
> grooms folder with the modified files, then it worked. The topology
> contained the new parameters. I guess there might be sth with how pdb2gmx
> finds the database files.

The proper approach for making local modifications is to create a complete force 
field directory with all necessary files within it.  The residuetypes.dat file 
must be in the working directory, not any subdirectory thereof, and you must 
issue all commands from within that directory.  Otherwise, Gromacs programs 
revert to the copy in $GMXLIB.  I suspect any of these factors will explain what 
you're observing with respect to intermittent successes - you're either moving 
around directories or putting files in the wrong place(s).



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


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