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

[Justin Lemkul]

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 
CHARMM and GROMACS.

-Justin

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

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