Dear GMX users Could you tell me how to make the topology file for ammonia in tip4p water?
I made topology file for ammonia by hand, as shown at end. MD dose work when system has only ammonia molecules. For ammonia in water, I had though it needed to add just two line at the top of .top file. ------------------------ #include "ffoplsaa.itp" #include "tip4p.itp" ------------------------ However, I got "Invalid order for directive defaults" in using grompp_d. Should I add this new atoms information into ffnonbonded.itp directly ?? ------------------------ ;[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon FN FN 0.0000 0.0000 A 3.39000e-01 1.414192e+00 FH FH 0.0000 0.0000 A 0.00000e+00 0.00000e+00 [ moleculetype ] ; Name nrexcl AM 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 FN 1 AM N 1 -1.03500 14.000000 2 FH 1 AM H1 3 0.34500 1.000000 3 FH 1 AM H2 4 0.34500 1.000000 4 FH 1 AM H3 5 0.34500 1.000000 [ bonds ] ; ai aj funct r k 1 2 1 1.0124e-01 5.0242e+05 1 3 1 1.0124e-01 5.0242e+05 1 4 1 1.0124e-01 5.0242e+05 [ pairs ] ; ai aj funct [ angles ] ; ai aj ak funct theta cth 2 1 3 1 1.0670e+02 6.2802e+02 2 1 4 1 1.0670e+02 6.2802e+02 3 1 4 1 1.0670e+02 6.2802e+02 [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 [ system ] ammonia [ molecules ] AM 11 ------------------------ K.Mochi -- 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