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On 11/11/2011 3:01 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopw-vgyeV18jeaaEUMErrWBy2JH0L7rbh-5vpdMn95aemw@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
I've no idea what any of the above was intended to mean. I'll repeat
myself again, there's nothing about the improper dihedrals that
enforces a particular chirality. Proper dihedrals also don't care
about chirality. Chirality is set in the starting configuration, and
merely preserved by the force field.<br>
<br>
<blockquote
cite="mid:CAALQopw-vgyeV18jeaaEUMErrWBy2JH0L7rbh-5vpdMn95aemw@mail.gmail.com"
type="cite"><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>
</blockquote>
<br>
See the #defines in ffbonded.itp. The implementation of the GROMOS
force fields are a bit idiosyncratic this way.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopw-vgyeV18jeaaEUMErrWBy2JH0L7rbh-5vpdMn95aemw@mail.gmail.com"
type="cite">
<br>
It could be cool that in that section such information present :)
<br>
<a moz-do-not-send="true"
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
moz-do-not-send="true" 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>
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