On 11/11/2011 3:17 AM, Thomas Piggot wrote:
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.
Good thought :-) I finally see what my brain was missing - the angle of
the improper dihedral is signed, and the relevant square is outside the
brackets so the sign matters. The order in which the atoms are specified
determines the sign of the angle. So molecules with opposite-sense
chiral centres do need different topologies.
Mark
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
2011/11/10 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
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.
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
