[gmx-users] modify H atom type from opls_369
sudheer.pbm07 at gmail.com
Sat Mar 29 05:49:37 CET 2008
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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