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

maria goranovic mariagoranovic at gmail.com
Tue Mar 29 11:51:35 CEST 2011

Just curious, this would also hold true for the OPLA-AA force field. It is
all-atom, so no changes seems to be necessary besides making a d-amino acid
in the input ?

On Mon, Mar 28, 2011 at 2:13 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 28/03/2011 8:45 PM, maria goranovic wrote:
> That would mean that a new residue type will not be required? I just need
> the correct input D-coordinates?
> Try it, before asking about it :-) I said "I suspect you do not need to
> change anything about the topology", but I haven't actually done anything
> like this ever. Topologies and code shouldn't care about chirality, so you
> shouldn't need to do anything other than input the configuration you want.
> Mark
>  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
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Maria G.
Technical University of Denmark
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