[gmx-users] modify H atom type from opls_369

sudheer babu sudheer.pbm07 at gmail.com
Sat Mar 29 05:49:37 CET 2008

Hi all,
Thanks for the response.

I used OPLS-AA/L force field for POPC and Protein
I calculated  the sigma and epsilon values as the way Mr.Justin mentioned in
yesterday reply , the values I got are
 ;name   name   charge     mass   charge   ptype    sigma           epsilon
  LO      LO         1        15.9994   0.000      A    0.295999914
0.878694594 ;carbonyl O, OPLS
  LOM   LOM      1        15.9994   0.000      A     0.295999914
0.878694594 ;carboxyl O, OPLS
  LNL    LNL        1        14.0067   0.000     A     3.35300e-03
3.95100e-06 ;Nitrogen, OPLS
  is it correct?

 Then in First step of Chris procedure(web link quoted below), suggested
that add atom type H from opls_369 to match H expected by pope.itp

 In archives this type of problem posted for pope type of lipids
  opls_369   H    1   1.008  0.400     A     0.0000e+00   0.0000e+00 (for
 Im using POPC type of lipid
 I want to ask two things
1.  How to modify H atom type in popc.itp file

2. Mr. Chris mentioned that Parameters require a double pairs section,  how
can I mention?

Pls give me detail explanation
all comments will be appreciated
Thanks in advance

>Yes, the LO LO in atom type should be as Justin has mentioned.
>Sudheer, please note that the original post that you quote below actually
includes an example for LO LO
  > "LO       LO     1    15.9994      0.000       A    2.96000e-01

>Also note that similar information is available in that post for pairtypes.
>Also note that these parameters require a double pairs section. Please do a
search for my posts on this method and read them carefully.


--- original message ---

> > Hi all ,
> > I wanted to use OPLS-FF for POPC and Protein, I followed the procedure
> > archives and the link is
> > *http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html*
> > The steps I have done are
> > 1. I added "atom types" from lipid.itp to ffoplsaanb.itp  here I got  no
> > exponential values for "sigma" and positive exponential "epsilon" values
> > when substituted in equations.
> > (atom types)
> >   ;name  name  charge  mass  charge  ptype  sigma        epsilon
> >    LO    LO      1  15.9994   0.000   A     0.00011209814
> > 2.90868792E+17;carbonyl O, OPLS

>I think you have done your calculations wrong.  Check the formulas again
>provided in Chris' post.  For example, if I calculate sigma and epsilon
>according to his equation, I get:

>sigma = 0.2959999302
>epsilon = 0.8786943396

>which seem much more reasonable, given the magnitudes of sigma and epsilon

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