Keith Callenberg wrote:
Hello gmx-users,
I wrote a script to perform a simulation on my Ubuntu 10.04 machine
running Gromacs 4.0.7. At the beginning of the script I convert the
system from pdb coordinates to gro using pdb2gmx. I am using the
GROMOS 45a3 forcefield, specified by -ff G45a3 and it works great.
pdb2gmx -f na.0.pdb -o na_initial.0.gro -ff G45a3 -water spce
However, when I move the script to a Mac OS X 10.6 machine running
Gromacs 4.5.4, I get the following error:
Fatal error:
Could not find force field 'G45a3' in current directory, install tree,
or GMXDATA path
Force field organization has changed completely since the 4.0.x series; the
proper name is now gromos45a3 instead of G45a3.
The forcefield is definitely on the system and works perfectly if I
don't specify the -ff argument, and instead use the interactive
selection. I even copied the file to the local working directory, put
it in a subdirectory named G45a3.ff (as described in the
documentation) and still got the error.
What was "the file" that you copied? The minimal requirements for pdb2gmx to
recognize a force field (but not necessarily work) are:
1. a properly named <something>.ff directory
2. a file named "forcefield.itp" in the <something>.ff directory
3. a file named "forcefield.doc" in the <something>.ff directory (maybe, I can't
remember if it's strictly required)
I also tried modifying the GMXDATA path (it was blank) to the path
that contains ffG45a3.itp in /usr/share. No luck there either.
Anything named ffG45a3.itp is retained only for compatibility in the newer
version and should simply #include "gromos45a3.ff/forcefield.itp" and nothing more.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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