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

Erik Marklund erikm at xray.bmc.uu.se
Tue Mar 29 11:54:54 CEST 2011

The best way to find out is by looking at the dihedrals fpor the 
aminoacid as defined by the forcefield. Someone may know it by heart, 
but to make sure you need to check it yourself anway. It'll be hard to 
defend your results before a picky referee by saying that "this dude on 
a mailing list said so".


maria goranovic skrev 2011-03-29 11.51:
> 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 
> <mailto: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 <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
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> Maria G.
> Technical University of Denmark
> Copenhagen

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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