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

[maria goranovic]

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
>>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110329/e3f2ae74/attachment.html>