On 9/21/16 1:43 AM, HENRY WITTLER wrote:
Greetings.


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

--
==================================================

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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