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