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

[maria goranovic]

Yes, that would be the correct way to do this. I was hoping to take a
shorter route, and just modifying a couple of dihedrals in the topology
files output by pdb2gmx without having to make a new residue. Is that not
possible at all ?



On Fri, Mar 25, 2011 at 12:24 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> Hi Maria,
>
> The general solution is to copy the entry in the .rtp file, modify the
> dihedrals involved, and rename the entry to match the name used in the
> coordinate (pdb) file. You may also need to copy the entries in the
> .hdb file, as well as the .tdb files if it is a terminal residue.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic
> <mariagoranovic at gmail.com> wrote:
> > 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
> >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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