[gmx-users] ffoplsaabon.itp help

Pawan Babel pwnbabel at chem.iitb.ac.in
Sun Oct 24 11:28:33 CEST 2004

Hello gmx-users,

Can anyone explain me why the order of the naming in ffoplsaabon.itp for
i,j ,k,l is different than usual convenction i.e. "i" is connected to "j"
and "j" is connected "k" and "k" is connected to "l" and finally (i-j-k-l)
forms a dihedral angle ?

According to .../gromacs/top/ffoplaabon.itp

 [ dihedraltypes ]
;  i    j    k    l   func     coefficients
; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form
; according to the formula in the Gromacs manual.
 C_3    CT_2   N      C       3    -10.35749 -29.58716  -1.16734  41.11199
  0.00000   0.00000 ; C-term phi.

 C      CT     CT_2   NT      3      3.33465  -1.55226   2.82001  -4.60240
  0.00000   0.00000 ; H2N terminal


According to me, it should be other way round either C_3 C N CT_2
(i-j-k-l) or CT_2 N C C_3 for C-terminal phi. So that it forms a proper
dihedral angle.
And similarly CT_2 C NT CT or CT NT C CT_2 for N-terminal.

Please correct me if i am wrong and also tell me how can i calcute these
fourier constants. According to E(torsional)= Summation [v0 *(1+cos(phi))
+v1 * (1- cos(2*phi)) + v2 *(1 +cos(3*phi)]
where v0,v1,v2 are fourier coefficients in kcal/mol.
 but from where we are getting v3,v4,v5 coefficients terms in

Thanks in advance
Pawan Babel

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