[gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA

ABEL Stephane Stephane.ABEL at cea.fr
Fri Mar 9 12:55:12 CET 2018

Dear all, 

I am constructing a top file for gramicidin A a short that contains a succession of D- and L-AAs (the exact sequence is HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH) and have a unexpected problem whenI use  charmm36 . Indeed it seems that a dihedral parameter is missing in the last charmm36m release for GROMACS but also (?) in the original last CHARMM toppar file (including CHARMM36m). For instance for linking the (D-LEU --> L-TRP) I need the CTD1  C  NH1 CT1 (where the CTD1 is the carbon atom type for D-LEU) however I did not find this parameters in the CHARMM36. 

Am I missing something or did something wrong ?? It is valid to use the values of CTD1  C  NH1 CT1.

Thanks in advance 


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