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<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000">Dear Users, </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000"> </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000">I am trying to port the new parmbsc0 forcefield (</font><a href="http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0"><font color="#000000">http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0</font></a><font color="#000000">) into gromacs for DNA simulations. </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000">While unit conversions are sufficient to convert many of the parameters from AMBER to GROMACS format, dihedral angle conversion does not seem to be straight forward - the dihedral parameters need to be converted to the Ryckaert-Bellemans parameters. I went through the GROMACS 4.0 manual, especially equations 4.61-4.65 to understand the procedure. The procedure involves comparing the fourier expansion of the IUPAC convention of dihedral potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62) to get the Cn's of the RB function. However, I am not able to understand how to account for the phase angles. (Also to note, the parmbsc0 forcefield contains phase angles other than 0 and 180.)</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000"> </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000"> Any advice or suggestion will be of great help. </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000"> </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000">Thank you, </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #c00000; FONT-SIZE: 10pt"><font color="#000000">Vignesh</font></span></p></div>
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<div>-- <br>R.Vigneshwar<br>Graduate Student,<br>Dept. of Chemical & Biomolecular Engg,<br>National University of Singapore,<br>Singapore<br><br>"Strive for Excellence, Never be satisfied with the second Best!!"<br>
<br>I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)<br></div>