[gmx-users] improper dihedral and proper dihedral
dong at pampas.chem.purdue.edu
Tue Feb 22 22:50:51 CET 2005
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
Have a nice day!
Dongsheng Zhang <dong at pampas.chem.purdue.edu>
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