[gmx-users] gromacs impropers

[alexander yakovenko]

Dear all,
Does anybody know about improper torsions in gromacs?
I have the system:
    CH3(C0)
     |
     CH2(C1)
     |
    CB(C2)=CH(C7)-CH(C6)   
     |                        ||    
    CH(C3)=CH(C4)-CH(C5)
      
Its work well, while I don t add C4-C3-C2-C1  improper angle.
 From  semiempirical AM1 dynamic I know, that this angle is 0, but adding this information to gromacs topology reduce to wrong simulation (the correct simulation is AM1 dynamic). After  energy minimization the angle C4-C3-C2-C1 is more than 30 degrees.
Why?

The impropers topology of this molecule is:
[ impropers ]
 C4  C3  C2  C1  0.00   500.00
 
 C2  C3  C7  C1  0.00   500.00  
 C2  C3  C4  C5  0.00   500.00
 C3  C4  C5  C6  0.00   500.00
 C4  C5  C6  C7  0.00   500.00
 C5  C6  C7  C2  0.00   500.00
 C6  C7  C2  C3  0.00   500.00  
 C7  C2  C3  C4  0.00   500.00

Thank you.

Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
03143
acad.Zabolotnogo str. 150
Kiev
Ukraine
______________________________________________
E-mail: yakovenko_a at ukr.net