Thomas, thank you!<br><br>It's my inattention so I've missed DALA in the rtp file :(<br><br>So as I've understood the difference just in one string<br> CA N C CB gi_2 for L form<br>CB N C CA gi_2 for D form<br>
<br><br>:D<br><br>James <br><div class="gmail_quote">2011/11/10 Thomas Piggot <span dir="ltr"><<a href="mailto:t.piggot@soton.ac.uk">t.piggot@soton.ac.uk</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;">
Hi James,<br>
<br>
I suggest to see the differences in topologies for L and D amino acids (in the GROMOS force fields at least) you look in the aminoacids.rtp file and in particular the differences between the ALA and DALA entries.<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
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 -C N CA C gd_39 N CA CB CG gd_34 N CA C +N gd_40 CA CB CG CD1 gd_34 <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" target="_blank">http://www.gromacs.org/<u></u>Documentation/Terminology/<u></u>Dihedral?highlight=dihedral</a><br>
<br>
<br></div>
2011/11/10 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>><div class="im">
<br>
<br>
First, identify that there's anything to invert. Look at the #define<br>
lines for gi_1 and gi_2 and the manual sections for impropers.<br>
There's nothing associated with any handedness. The impropers for<br>
chirality prevent inversion, rather than enforcing a particular<br>
chirality. You can test this yourself. Make a .tpr of an L-amino<br>
acid and .gro files of each chirality, and then use mdrun -rerun<br>
Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun<br>
Rconfiguration.gro -s Lconfiguration.<br>
<br>
<br>
</div></blockquote><font color="#888888">
<br>
-- <br>
Dr Thomas Piggot<br>
University of Southampton, UK.</font><div><div></div><div class="h5"><br>
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