Thomas, thank you! It's my inattention so I've missed DALA in the rtp file :(
So as I've understood the difference just in one string CA N C CB gi_2 for L form CB N C CA gi_2 for D form :D James 2011/11/10 Thomas Piggot <[email protected]> > Hi James, > > I suggest to see the differences in topologies for L and D amino acids (in > the GROMOS force fields at least) you look in the aminoacids.rtp file and > in particular the differences between the ALA and DALA entries. > > Cheers > > Tom > > James Starlight wrote: > >> Mark, >> >> I've mistaken >> >> I need to invert impropers for DIHEDRAL for Calpha atom. By this way I >> want to change L form to D form for Gromos ff. Does this correct ? >> >> [ dihedrals ] >> ; ai aj ak al gromos type >> -CA -C N CA gd_14 -C N CA C gd_39 >> N CA CB CG gd_34 N CA C +N gd_40 CA >> CB CG CD1 gd_34 >> >> So I think that I need to make corrections in that gd_n files. But in >> what exactly and where in manual could I read about that parametrisation ? >> >> It could be cool that in that section such information present :) >> http://www.gromacs.org/**Documentation/Terminology/** >> Dihedral?highlight=dihedral<http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral> >> >> >> 2011/11/10 Mark Abraham <[email protected] <mailto: >> [email protected].**au <[email protected]>>> >> >> >> First, identify that there's anything to invert. Look at the #define >> lines for gi_1 and gi_2 and the manual sections for impropers. >> There's nothing associated with any handedness. The impropers for >> chirality prevent inversion, rather than enforcing a particular >> chirality. You can test this yourself. Make a .tpr of an L-amino >> acid and .gro files of each chirality, and then use mdrun -rerun >> Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun >> Rconfiguration.gro -s Lconfiguration. >> >> >> > -- > Dr Thomas Piggot > University of Southampton, UK. > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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