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

[Justin Lemkul]

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

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