Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I followed the chris neale directives to make the necessary changes i.e. sigma and epsilon, I incorporated the modified atom types of lipids in oplsaanb_lipid.itp LO LO 1 15.9994 0 A 0.29599993 0.87869434 ;carbonyl O, OPLS" LOM LOM 1 15.9994 0 A 0.29599993 0.87869434 ;carboxyl O, OPLS
I also made changes to the [pair types] and appended them in the oplsaanb_lipid.itp file [ pair types ] ; i j func sigma epsilon LO LO 1 0.29603763 0.10964147 LO LOM 1 0.29603763 0.10964147 LO opls_116 1 0.306316902 0.094663158 and also changed the OW to opls_116 and removed HW lines. Now I want to generate the tpr file using grompp where I had generated a topol_popc.top : -------------------------------------------------------------------------------------------------- ; Include chain topologies #include "oplsaa_lipid.ff/forcefield.itp" #include "popc.itp" ; Include water topology #include "oplsaa_lipid.ff/spc.itp" ; System specifications [ system ] 128-Lipid POPC Bilayer [ molecules ] ; molecule name nr. POPC 128 SOL 2460 --------------------------------------------------------- Now when I run the grompp command it gives me following error: ERROR 1 [file ffoplsaanb_lipid.itp, line 852]: Invalid directive pair types WARNING 1 [file ffoplsaanb_lipid.itp, line 854]: Too few parameters on line (source file toppush.c, line 246) ----- Generated 359128 of the 359128 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 359128 of the 359128 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' There were 91 warnings ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1372 Fatal error: There was 1 error in input file(s) I am not able to get where I am going wrong. Thanking you, Parul -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
