[gmx-users] ffoplsaabon.itp help
pwnbabel at chem.iitb.ac.in
Sun Oct 24 11:28:33 CEST 2004
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
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
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