[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Mar 26 02:02:42 CET 2011
On 26/03/2011 2:27 AM, maria goranovic wrote:
> 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 ?
Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in a
general sense. It generates a topology that matches given coordinates,
fixing a few details as directed. It will fill valences with hydrogen
atoms, generate terminal groups, organize disulfides, and choose
protonation states of titratable residues, but it won't change
geometries in the way you seem to want.
Neither does anything in the .top/.itp files stipulate the chirality of
any center (in all-atom models). Various dihedral angles change sign
with chirality, but the dihedral functions are all symmetric about the
y-axis (i.e. even). So I suspect you do not need to change anything
about the topology. Just use a molecule builder to change the chirality
of the relevant center in the input file to pdb2gmx.
Mark
> On Fri, Mar 25, 2011 at 12:24 PM, Tsjerk Wassenaar <tsjerkw at gmail.com
> <mailto: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 <mailto: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 <mailto: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 <mailto: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
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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
> --
> gmx-users mailing list gmx-users at gromacs.org
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>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
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