Mark,<br><br>I've mistaken<br><br>I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ?<br><br> [ dihedrals ]<br>; ai aj ak al gromos type<br>
-CA -C N CA gd_14 <br> -C N CA C gd_39 <br> N CA CB CG gd_34 <br> N CA C +N gd_40 <br> CA CB CG CD1 gd_34 <br><br><br>So I think that I need to make corrections in that gd_n files. But in what exactly and where in manual could I read about that parametrisation ?<br>
<br>It could be cool that in that section such information present :) <br><a href="http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral">http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral</a><br>
<br><br><div class="gmail_quote">2011/11/10 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#FFFFFF" text="#000000">First, identify that there's anything to invert. Look at the #define
lines for gi_1 and gi_2 and the manual sections for impropers.
There's nothing associated with any handedness. The impropers for
chirality prevent inversion, rather than enforcing a particular
chirality. You can test this yourself. Make a .tpr of an L-amino
acid and .gro files of each chirality, and then use mdrun -rerun
Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun
Rconfiguration.gro -s Lconfiguration.<br><font color="#888888">
</font><br></div></blockquote></div><br>