[gmx-users] AMBER force fields in gromacs program
karami.leila1 at gmail.com
Tue Oct 20 13:54:36 CEST 2009
I want to use AMBER force fields in gromacs program for md simulation of
pr-dna interaction . I did works said in
*installation & Testing:*
(1) Install the desired GROMACS
<http://www.gromacs.org/>distribution (v3.1.4, v3.2.1, v3.3, or
(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
(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
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
/usr/local/bin/GMXRC: line 44: CSH:: command not found
/usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token
/usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv
please help me.
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