>From ffamber (in e.g. .../gromacs/top/ffamber99sbbon.itp):<div><br></div><div>- impropers treated as propers in GROMACS to use correct AMBER analytical function</div><div>- propers treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet</div>
<div><br></div><div>I followed these instructions while building acpypi (<a href="http://acpypi.googlecode.com/">acpypi.googlecode.com/</a>).</div><div><br></div><div>You can study my code and see how the conversion is done (I put the details inside acpypi.py).</div>
<div><br></div><div>I didn't test acpypi with an amber prmtop/inpcrd input with parmbsc0 parameters, but it would be interesting to see what I would get.</div><div><br></div><div>Bear in mind that if parmbsc0 were "simple" to port, then it would have been done since the first version of ffamber, but I know Eric Sorin is working on that now.</div>
<div><br></div><div>Alan<br><br><div class="gmail_quote">On Wed, Apr 7, 2010 at 22:00, <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=":vu" class="ii gt">> Dear Users,<br>
><br>
> 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<br>
> from AMBER to GROMACS format, dihedral angle conversion does not seem to<br>
> be straight forward - the dihedral parameters need to be converted to<br>
> the Ryckaert-Bellemans parameters.<br>
<br>
Why? GROMACS can probably do the non-RB form - IIRC you can implement a<br>
sum of multiple instances of 4.61 with different n.<br>
<br>
> I went through the GROMACS 4.0<br>
> manual, especially equations 4.61-4.65 to understand the procedure. The<br>
> procedure involves comparing the fourier expansion of the IUPAC<br>
> convention of dihedral potential (equation 4.65) with the<br>
> Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62)<br>
> to get the Cn's of the RB function. However, I am not able to understand<br>
> how to account for the phase angles. (Also to note, the parmbsc0<br>
> forcefield contains phase angles other than 0 and 180.)<br>
<br>
Elegant conversion formulae require those angles to be convenient...<br>
<br>
Mark<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>
</div>