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 pope) 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 8.87864e-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. Chris. --- original message --- > > > > Hi all , > > I wanted to use OPLS-FF for POPC and Protein, I followed the procedure from > > 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 from >ffoplsaanb.itp. -Justin
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