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.
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