Dear Justin Thank you for reply.
I added #include "ffoplsaa.itp" into top and #include "tip4p.itp" after [exclusions], as you told. Then, I could make tpr file and MD looks working. Thank you very much. Kenji ----- Original Message ----- >> From: Justin Lemkul <[email protected]> >> To: Discussion list for GROMACS users <[email protected]> >> Date: 2012-12-06 22:56:19 >> Subject: Re: [gmx-users] How to merge Self-made ammonia .top with tip4p >> >> >> On 12/6/12 6:09 AM, Kenji Mochizuki wrote: >> > 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 ?? >> > >> >> That should not be necessary. If your [defaults] directive is properly >> commented out (as shown), you shouldn't get this error. >> >> The order of inclusion is important. You have to define all force >> field-level >> directives (e.g., [defaults], [atomtypes], etc) before you can define any >> [moleculetypes], so you can't #include "tip4p.itp" until after the ammonia >> parameters, since you're introducing new [atomtypes] for that molecule. The >> easiest solution is simply to move that #include statement right after the >> end >> of the ammonia [moleculetype] definition (see below). >> >> > ------------------------ >> > ;[ 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 >> >> Add #include "tip4p.itp" here. >> >> -Justin >> >> > [ system ] >> > ammonia >> > [ molecules ] >> > AM 11 >> > ------------------------ >> > >> > K.Mochi >> > >> > >> >> -- >> ======================================== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> ==================== National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: [email protected] phone: 0564-55-7394 ==================== -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
