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

Payman Pirzadeh ppirzade at ucalgary.ca
Wed Jan 9 02:32:16 CET 2013

Dear Justin,
You are absolutely right. I only needed to keep the modified
'residuetypes.dat' in my working directory not the .rtp and .hdb files. I
retried the whole process and this time CYA was not a separate group. Great
Thanks for your patience and help.


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin Lemkul
Sent: January-08-13 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

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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