[gmx-users] Re: AMBER force fields in gromacs program

Alan alanwilter at gmail.com
Tue Oct 20 14:10:48 CEST 2009

Please, let me suggest you acpypi.googlecode.com. There you'll find in
the wikis help about installing gromacs 4.0.5 with support for


On Tue, Oct 20, 2009 at 12:55,  <gmx-users-request at gromacs.org> wrote:
> Hi
> I want to use AMBER force fields in gromacs program for md simulation of
> pr-dna interaction . I did  works  said  in
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/AMBER
> *installation & Testing:*
>          (1) Install the desired GROMACS
> <http://www.gromacs.org/>distribution (v3.1.4, v3.2.1, v3.3, or
> v3.3.1).
>  (2) Download the appropriate ffamber ports (.tar.gz) with or without pdf
> documentation from the table below, being sure that the version number you
> choose matches the version of GROMACS you are using.
>  (3) Unzip/untar the downloaded tar.gz file.
>  (4) Copy aminoacids.dat and vdwradii.dat to the "top" directory in your
> gromacs distribution (you should see force field files there, such as
> ffoplsaa.*). If you plan on simulating nucleic acids, refer to the note for
> nucleic acids in
> aminoacids.dat<file:///home/leila/Desktop/ffAMBER%20Homepage#aadat>below.
>  (5) Files for each force field are located in a seperate subdirectory, such
> as ffamber94/ for the Cornell potential. Copy the desired ffamber* files to
> the top directory in your gromacs distribution.
>  (6) Increment the number at the top of the "top/FF.dat" file by 1 for each
> AMBER port you'll install (so that it matches the total number of
> forcefields available in the "top" directory).
>  (7) Add lines like the following to the "top/FF.dat" file. These are used
> by pdb2gmx to allow you to identify the desired FF and field 1 must match
> the ffamber* filename prefixes, whereas the following fields can be
> user-defined:
>     ffamber94 AMBER94 Cornell protein/nucleic forcefield
>     ffamber99 AMBER99 Wang protein/nucleic acid forcefield
>     ffamber99p AMBER99p protein/nucleic forcefield
>     ffamber03 AMBER03 Duan protein/nucleic forcefield
>  (8) Locate the GMXRC in your GROMACS distribution and run `source GMXRC`.
>  (9) Run `pdb2gmx -H14 -f any.pdb` with any pdb to verify that these force
> fields are now seen by GROMACS. Working example .pdb files are available
> below, alongside pre-prepared gro and top files (GROMACS 3.1.4 / AMBER94) to
> which you can compare your resulting files.
> I did step 8 (runing of GMXRC) but :
> /usr/local/bin/GMXRC: line 35: return: can only `return' from a function or
> sourced script
> /usr/local/bin/GMXRC: line 44: CSH:: command not found
> /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token
> `setenv'
> /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv
>  please help me.
> thanks alot

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)

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