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

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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