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 ffamber.
Cheers, Alan On Tue, Oct 20, 2009 at 12:55, <gmx-users-requ...@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 > LD_LIBRARY_PATH ""' > > 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) _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
