If anyone can give insight please.
I want to do a MD for insulin a 51aa protein, mutating one residue from L to
I have runned 1.5us for the L- Ser (with cmap), and want to repeat it for the
D-Ser, with gmx v.5.0.4 charmm36 mars14 version.
It seems in the traditional CHARMM one have to change dihedrals involved with
changing L- to D-
also the cmap is for L-aa
In link http://www.swisssidechain.ch/D_residues.php gives topology D-aa for
gmx-charmm, without changing anything about cmap.itp, only .hdb and .rtp.
and my own testing MD and looking at it in vmd etc, seems to imply that the
.top, .itp do not distinguish about chirality, is this the case?
How is cmap.itp implemented in gmx, is these parameters for L-, and D-
Phd in Molecular modelling group (Brian J. Smith)
Department of Chemistry and Physics, La Trobe Institute for Molecular Science,
La Trobe University, Victoria 3086, Australia
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