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

[maria goranovic]

Hi

Appreciate the quick help

I am sorry, this is not an improper, but a proper dihedral that holds the
chirality in place. Then the solution suggested by Meli would not work? I do
not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So
the question is simply how to set the proper chirality to a D-amino acid in
CHARMM.



Maria

On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> 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
> --
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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