Does anyone know why lipid.itp contains [pairtypes] LJ-1,4 values including lipid atoms and OW or HW? I can understand their inclusion in [nonbond_params], but it seems as if this would never be required in [pairtypes].
*** In case anyone else is trying to merge lipid.itp and OPLSAA, here is what I have done. There is no type of guarantee here, just a listing of what appears to be working so far for me. Download lipid.itp and pope.itp (or your lipid) from http://moose.bio.ucalgary.ca/ kindly made available for all by Dr. Peter Tieleman. 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) 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. 3. Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp. - Prior to running ensure that the non-RB dihedral does not exist for these groups. 4. make a topology file like this: #include "ffoplsaa.itp" #include "myprotein.itp" #include "spc.itp" #include "pope.itp" [ system ] system_name [ molecules ] ; Compound #mols Protein 1 POPE 299 SOL 8991 _______________________________________________ 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
