[gmx-users] pdb2gmx Could not find force field, when using -ff commandline parameter

[Justin A. Lemkul]

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

-- 
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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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