<font size="4">Hi<br>I want to use AMBER force fields in gromacs program for md simulation of pr-dna interaction . I did works said in </font><pre><font size="4"><a href="http://www.gromacs.org/Documentation/Terminology/Force_Fields/AMBER">http://www.gromacs.org/Documentation/Terminology/Force_Fields/AMBER</a><br>
</font><br><br><font size="4"></font><b><big><a name="install" id="install">installation & Testing:</a></big></b><br> <br> </pre><table border="0" cellpadding="2" cellspacing="1" width="100%">
<tbody>
<tr>
<td valign="top">(1)</td>
<td style="text-align: left;">Install the desired
<a target="_blank" href="http://www.gromacs.org/">GROMACS</a> distribution
(v3.1.4, v3.2.1, v3.3, or v3.3.1).</td><td valign="top"><br></td>
</tr>
<tr>
<td valign="top">(2)</td>
<td style="text-align: left;">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.</td><td valign="top"><br></td>
</tr>
<tr>
<td valign="top">(3)</td>
<td style="text-align: left;">Unzip/untar the
downloaded tar.gz file.</td><td valign="top"><br></td>
</tr>
<tr>
<td valign="top">(4)</td>
<td style="text-align: left;">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 <a href="file:///home/leila/Desktop/ffAMBER%20Homepage#aadat">note for nucleic acids in
aminoacids.dat</a> below.</td><td valign="top"><br></td>
</tr>
<tr>
<td valign="top">(5)</td>
<td style="text-align: left;">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.</td><td valign="top"><br></td>
</tr>
<tr>
<td valign="top">(6)</td>
<td style="text-align: left;">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).</td><td valign="top"><br></td>
</tr>
<tr>
<td valign="top">(7)</td>
<td style="text-align: left;">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:<br>
ffamber94 AMBER94
Cornell protein/nucleic forcefield<br>
ffamber99 AMBER99
Wang protein/nucleic acid forcefield<br>
ffamber99p AMBER99p
protein/nucleic forcefield<br>
ffamber03 AMBER03
Duan protein/nucleic forcefield</td><td valign="top"><br></td>
</tr>
<tr>
<td valign="top">(8)</td>
<td style="text-align: left;">Locate the GMXRC in
your GROMACS distribution and run `source
GMXRC`.</td><td valign="top"><br></td>
</tr>
<tr>
<td valign="top">(9)</td>
<td style="text-align: left;">
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.<br><br>I did step 8 (runing of GMXRC) but :<br><br>/usr/local/bin/GMXRC: line 35: return: can only `return' from a function or sourced script<br>/usr/local/bin/GMXRC: line 44: CSH:: command not found<br>
/usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv'<br>/usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""'<br><br> please help me.<br>
thanks alot<br></td><td valign="top"><br></td></tr></tbody></table><pre><br><font size="4"><br></font><br></pre>