[gmx-users] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation

[Parul tew]

Dear GMX users,
 I am working on a protein which I want to simulate in a lipid bilayer
environment (POPC) and want to use OPLS force field for the same. I wanted
to modify the parameter files of lipids taken from peter teilman site.
Taking cue from chris neale (may 2006 gmx mailing list) I changed the c6
and c12 to sigma epsilon using formula
Sigma = (c12/c6)^1/6
and
epsilon = c6/(4*sigma^6)
i tried it for the [pairtypes] in lipid.itp file, but the calculations I
made using excel gave me the following:

[ pairtypes ]
;       i       j       funct   sigma           epsilon
        LO      LO      1       1.10E-01        2.96E-01
        LO      LOM     1       1.10E-01        2.96E-0


and so on i.e. the values of sigma and epsilon are interchanged, as
opposed to the values listed by chris neale in archive mail (listed
below)

[ pairtypes ]

;       i       j       funct   sigma           epsilon
        LO      LO      1       2.96E-01        1.10E-01
        LO      LOM     1       2.96E-01        1.10E-01
        LO      opls_116        1       3.06E-01        9.47E-02
        LO      LNL     1       3.10E-01        9.88E-02
        LO      LC      1       3.33E-01        7.76E-02
etc...

I am doing something wrong or I can just interchange the values and
use them accordingly.

Thanking you

Parul Tewatia