[gmx-users] CMAP entries for D-residues with GROMACS

Justin Lemkul jalemkul at vt.edu
Fri Mar 2 16:53:24 CET 2018

On 3/2/18 10:50 AM, ABEL Stephane wrote:
> Dear all,
> I am interested to simulate a system with gramicidin A  that contains D-AAs (D-LEU and D-VaL)  and I am wondering if the CMAP entries in the cmap.itp file (charmm36-jul2017.ff) are used for these types of AA ? I am asking this because I see that the CHARMM force field library contains a file (toppar_all36_prot_mod_d_aminoacids.str) where the CMAP parameter seem to be redefined.

The parameters are not "redefined," they are given for the D-amino 
acids, which have a different C-alpha type (CTD1 instead of CT1). The 
latest CHARMM36 port supports D-amino acids, with the exception of the 
.hdb file, which does not have entries for them.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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