Hi all, <br>Thanks for the response.<br><br>I used OPLS-AA/L force field for POPC and Protein<br>I calculated the sigma and epsilon values as the way Mr.Justin mentioned in yesterday reply , the values I got are<br> ;name name charge mass charge ptype sigma epsilon<br>
LO LO 1 15.9994 0.000 A 0.295999914 0.878694594 ;carbonyl O, OPLS<br> LOM LOM 1 15.9994 0.000 A 0.295999914 0.878694594 ;carboxyl O, OPLS<br> LNL LNL 1 14.0067 0.000 A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS<br>
is it correct?<br><br> 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<br><br> In archives this type of problem posted for pope type of lipids<br>
opls_369 H 1 1.008 0.400 A 0.0000e+00 0.0000e+00 (for pope)<br>
Im using POPC type of lipid<br> I want to ask two things<br>1. How to modify H atom type in popc.itp file<br><br>2. Mr. Chris mentioned that Parameters require a double pairs section, how can I mention?<br><br>Pls give me detail explanation <br>
all comments will be appreciated
<br>Thanks in advance<br><br><br>>Yes, the LO LO in atom type should be as Justin has mentioned.<br>
>Sudheer, please note that the original post that you quote below actually includes an example for LO LO<br>
> "LO LO 1 15.9994 0.000 A 2.96000e-01 8.87864e-01"<br>
<br>
>Also note that similar information is available in that post for pairtypes.<br>
>Also note that these parameters require a double pairs section. Please
do a search for my posts on this method and read them carefully.<br>
<br>
Chris.<br>
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--- original message ---<br>
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> > Hi all ,<br>
> > I wanted to use OPLS-FF for POPC and Protein, I followed the procedure from<br>
> > archives and the link is<br>
> > *<a href="http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html*" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html*</a><br>
> > The steps I have done are<br>
> > 1. I added "atom types" from lipid.itp to ffoplsaanb.itp here I got no<br>
> > exponential values for "sigma" and positive exponential "epsilon" values<br>
> > when substituted in equations.<br>
> > (atom types)<br>
> > ;name name charge mass charge ptype sigma epsilon<br>
> > LO LO 1 15.9994 0.000 A 0.00011209814<br>
> > 2.90868792E+17;carbonyl O, OPLS<br>
><br>
<br>>I think you have done your calculations wrong. Check the formulas again<br>
>provided in Chris' post. For example, if I calculate sigma and epsilon<br>
>according to his equation, I get:<br>
<br>
>sigma = 0.2959999302<br>
>epsilon = 0.8786943396<br>
<br>
>which seem much more reasonable, given the magnitudes of sigma and epsilon from<br>
>ffoplsaanb.itp.<br>
<br>
-Justin<br>
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