[gmx-users] improper dihedral and proper dihedral

[David]

On Tue, 2005-02-22 at 16:50 -0500, Dongsheng Zhang wrote:
> Dear David,
> 
> Thank you very much for your reply. After I study ffoplsaa.rtp and
> discuss with my colleague, I have better understanding with improper
> dihedrals. However, I still have some questions:
> 
> 1. If four atoms form an improper dihedral, only when the central atom
> is N or C (with double bonds), we will assign that improper dihedral in
> Gromacs. Is it correct? Could you please tell me how to make the
> sequence of those four atoms (The third one is the central, how about
> others?)? I think the sequence is important because we will use the
> outer two atoms to define the improper dihedral parameters (angle and
> constant) in *.itp (e.g. ffgmx2bon.itp).
> 
> 2. When I check ARGN in the file ffoplsaa.rtp, I found five impropers:
> 
> 
>  [ impropers ]
>     -C    CA     N     H    improper_Z_N_X_Y 
>     CA    +N     C     O    improper_O_C_X_Y 
>     CD    CZ    NE    HE    improper_Z_N_X_Y 
>     NE   NH1    NZ   NH2    improper_O_C_X_Y 
>     CZ  HH21   NH2  HH22    improper_Z_N_X_Y 
> 
>  I think there is a typo in the third improper dihedral, the third atom
> should be CZ, not NZ.
> 
> 3. It surprises me that there is no (proper) dihedral for ARGN in the
> file ffoplsaa.rtp. For most amino acids, there are two common dihedrals:
> 
>   N    CA    CB    CG     dih_***_chi1_N_C_C_C
>  CG    CB    CA     C     dih_***_chi1_C_C_C_CO
> 
> why does Gromacs not assign any dihedral to ARGN?
> 
> Could you please tell me how to decide which dihedrals we need to assign
> to Gromacs? 
> 
First this is defined by the force field, and I encourage you to read
the papers about OPLS.

Second, in the gromacs manual (ch. 4) there is a quite clear description
of improper dihedrals, which types there are etc.

Third, I assume ARGN is a neutral ARG? Please check it carefully before
using, and after using, by e.g. running a separate simulation of ARGN in
water (just the amino acid), and verify whether the conformations are
correct (errors in impropers often lead to atoms going out of plane
etc.)

If you, after testing conclude that there indeed are errors, then please
report so that we can fix it.
> 
> 
> Have a nice day!
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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