[gmx-users] D- &/or L- cmap for charmm36
jalemkul at vt.edu
Wed Sep 21 21:08:34 CEST 2016
On 9/21/16 1:43 AM, HENRY WITTLER wrote:
> 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?
The parameters provided are for L-amino acids. There are D-amino acid CMAP
parameters available in CHARMM, but not in GROMACS format. See the latest force
field distribution on http://mackerell.umaryland.edu/charmm_ff.shtml#charmm and
look in stream/prot/toppar_all36_prot_d_aminoacids.str
The D vs L stereochemistry is made possible by assigning a special atom type to
the CA atom (CTD1 instead of CT1) so you can apply residue-specific parameters.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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