I posted the procedure and not the modified files mostly because this is my modification of somebody else's files. Without permission, it is not reasonable for me to redistribute them. In order to both help you and still treat the originals with due respect, I have attached snippets that will help you to make your own modifications. It should not take very long for you to copy the procedure.
Regarding the advisability of combining the Berger lipids and the OPLS-AA force field... Read this: Tieleman et. al. J. Phys.:Condens. Matter 18 (2006) S1221-34 As for my own interpretation (of course that depends on your system and what question you are trying to answer): If you are focusing mostly on the protein and just want a pretty good lipid, then yes, I personally think it's a good combo. If you are focusing on the lipid behaviour around the protein then you run into more difficulty, but then again there really aren't any good fields for that as far as I know. I am not sure how good the Berger lipid / gromos field combination represents that either. Follow the procedure here: http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html When it says: 1. Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12 to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected by pope.itp - sigma = (c12/c6)^1/6 - epsilon = c6/(4*sigma^6) Do this: a) Using some script of your own or MS Excel convert the c6 and c12 values to sigma and epsilon values as per the noted equations. b) Take the [atomtypes] section from lipid.itp to the [atomtypes] section of ffoplsaanb.itp. Since ffoplsaanb.itp has only one section, and it is [atomtypes], just paste it to the bottom. When it says: 2. Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12 to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all reference to OW to opls_116 (opls spc water oxygen) and simply removed any with reference to HW as it will be zero regardless. Do this: c) Make the same c6/c12 -> sigma/epsilon changes and paste the section ([pairtypes] identifier and all) to the bottom of the new ffoplsaanb.itp file. When it says: 3. Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp. - Prior to running ensure that the non-RB dihedral does not exist for these groups. Do this: d) paste the following segment to the bottom of ffoplsaabon.itp: ; Added by Chris Neale April 16 2006 based on ; lipid.inp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies ; Based on Berger et al, Biophys. J. (1997) 72, pp. 2002-2013. ; Copy and paste from lipid.inp ;[ bondtypes ] ;[ constrainttypes ] ;[ angletypes ] [ dihedraltypes ] ; i j func coefficients LP2 LP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 etc... e) Then make your topology file according to what was already laid out in section 4 of the previous post. ############################# The relevant addition from my ffoplsaanb.itp file ; Added by Chris Neale April 16 2006 based on ; lipid.inp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies ; Based on Berger et al, Biophys. J. (1997) 72, pp. 2002-2013. ; Copy and paste from lipid.inp then duplicate first column and add zero in 3rd column ; Then comment out initial version (with C6 and C12) and replace with sigma and epsilon ; NOTE considered the use of epsilon LOS 0.711 (Berger/OPLS?) not 0.879 (Tieleman) ; HOWEVER, dihedrals etc are set up for 0.879 therefore use that one ; Also added name = H from opls_369 to match H expected by pope.itp ; Also changed 3rd column from all zeros to all ones LO LO 1 15.9994 0.000 A 2.96000e-01 8.87864e-01 ;carbonyl O, OPLS LOM LOM 1 15.9994 0.000 A 2.96000e-01 8.87864e-01 ;carbonyl O, OPLS LNL LNL 1 14.0067 0.000 A 3.25000e-01 7.11280e-01 ;Nitrogen, OPLS etc... ; Added by Chris Neale May 1 2006 based on ; lipid.inp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies ; Based on Berger et al, Biophys. J. (1997) 72, pp. 2002-2013. ; Copy and paste from lipid.inp into excel then convert c6 and c12 to sigma and epsilon ; sigma=power(c12/c6,1/6) and epsilon=c6/(4*power(sigma,6)) ; NOTE direct conversion therefore using LOS epsilon 0.879 as Tieleman ; Removed all SPC hydrogen as they will be calculated as zero anyway ; This was required so as to give LJ14 values involving lipid-lipid a fudgeLJ value of 0.125 [ 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... _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php