[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
Mon Mar 28 14:13:04 CEST 2011

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.


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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110328/cb02fda7/attachment.html>

More information about the gromacs.org_gmx-users mailing list