[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[Tsjerk Wassenaar]

Hi Maria,

The CHARMM force field is an all-atom one. That means it does not
require improper dihedrals to maintain chirality. If you have a D-ASP
in your structure file, you can rename it to ASP and just run pdb2gmx.
Mind not to regenerate hydrogens in that case, or make sure to modify
the hydrogen position for the D amino acids afterwards, to set the
proper chirality.

Hope it helps,

Tsjerk

On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic
<mariagoranovic at gmail.com> wrote:
> Hello List
> I want to change an ASP to a D-ASP. I think it should be possible by simply
> changing 2 improper values around the chiral carbon to their opposite sign.
> Instead of making a brand new residue, I thought I would take the topology
> of an ASP generated by pdb2gmx, and simply change values manually in the
> resulting .itp. However, this is not possible because gromacs wants to read
> the dihedral parameters from the ffbonded.itp file. Is it possible for me to
> explicitly state the parameters for these two dihedrals in my d-asp.itp
> file? This will be the fastest solution to the problem because it precludes
> making a new residue or defining new atoms types and so on. With the CHARMM
> force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3 which we
> are used to for gromos topologies.
> The mailing list search function was down, so I could not explore prior
> messages about this.
> --
> Maria
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands