<div>I strongly advice you to contact Eric Sorin from ffAMBER project as he's onto that and you maybe can add to his efforts.</div><div><br></div><div><a href="http://ffamber.cnsm.csulb.edu/">http://ffamber.cnsm.csulb.edu/</a></div>
<div><br></div><div>Alan</div><br><br><div class="gmail_quote">On Wed, Apr 7, 2010 at 11:00, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div id=":4rj" class="ii gt">I am trying to port the new parmbsc0 forcefield (<br>
<a href="http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0" target="_blank">http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0</a>) into gromacs for DNA<br>
simulations.<br>
<br>
While unit conversions are sufficient to convert many of the parameters from<br>
AMBER to GROMACS format, dihedral angle conversion does not seem to be<br>
straight forward - the dihedral parameters need to be converted to the<br>
Ryckaert-Bellemans parameters. I went through the GROMACS 4.0 manual,<br>
especially equations 4.61-4.65 to understand the procedure. The procedure<br>
involves comparing the fourier expansion of the IUPAC convention of dihedral<br>
potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of<br>
dihedral potential (equation 4.62) to get the Cn's of the RB function.<br>
However, I am not able to understand how to account for the phase angles.<br>
(Also to note, the parmbsc0 forcefield contains phase angles other than 0<br>
and 180.)<br></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>