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 LD_LIBRARY_PATH ""' please help me. thanks alot
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