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

Justin Lemkul jalemkul at vt.edu
Fri Mar 9 14:54:46 CET 2018

On 3/9/18 6:55 AM, ABEL Stephane wrote:
> 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.

Yes. The CTD1 atom type is just a clone of CT1, and the parameters for 
CT1-C-NH1-CTD1 are copied from CT1-C-NH1-CT1, so the parameters for 
CTD1-C-NH1-CT1 will also be the same as CT1-C-NH1-CT1. I'm not sure why 
that's never caused a problem before, but I'll get it fixed in both 



Justin A. Lemkul, Ph.D.
Assistant Professor
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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