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

[maria goranovic]

That would mean that a new residue type will not be required? I just need
the correct input D-coordinates?

On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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
>> >> >
>> >> > --
>> >> > 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
>> >> --
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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
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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