[gmx-users] D- &/or L- cmap for charmm36

HENRY WITTLER 17526019 at students.latrobe.edu.au
Wed Sep 21 07:43:20 CEST 2016


If anyone can give insight please.

I want to do a MD for insulin a 51aa protein, mutating one residue from L to D-Ser.

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- (http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/node4.html), also the cmap is for L-aa (http://mackerell.umaryland.edu/~kenno/cgenff/faq.php).

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.

Previous discussions (http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/r1t0ZqeF/converting-l-to-d-amino-acid-in-the-charmm-force-field-in-gromacs-where-to-alter-dihedral) 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- aminoacids?


Henry Wittler

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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