Hello, Just a reminder that I had troubled with combination rules between my water model and GROMACS forcefields. I fixed the problem by adjusting my water model's parameters. BUT, now, I specified the new parameters in my .itp file under [ atomtype ] category and grompp makes errors out of the orders. Now I am using OPLSaa. I suspect again the problem comes from the presence of the second [atomtype ]. How can I keep my new parameters and use them in my water model's itp file? Or should I change these parameters in the OPLSaa.itp file? Regards,
Payman On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote: > Paymon Pirzadeh wrote: > > I checked all the force-fields available in the GROAMCS. None of them > > have the #2 combination rule which matches my water model! Any > > alternatives (rather than changing my water model)? > > A water model that isn't compatible with the model of the solutes isn't > of any value, so it looks like you have put the cart before the horse. > > Mark > > > On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote: > >> Paymon Pirzadeh wrote: > >>> That was very helpful! But I realized a problem. The OPLSaa uses the > >>> combination rule #3 in [ defaults ] while my water model uses #2. Now if > >>> I comment out my water model's combination, I am not sure what I am > >>> going to face! Any comments? > >>> > >> Then I would say that your water model's combination rule is inconsistent > >> with > >> the method of nonbonded calculations in OPLS. It appears that the only > >> difference between combination rules 2 and 3 comes when a specific > >> interaction > >> is not defined in the [nonbond_params] section. The specifics of these > >> combination rules are given in manual section 5.3.3. > >> > >> -Justin > >> > >>> Payman > >>> > >>> > >>> > >>> > >>> On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote: > >>>> Paymon Pirzadeh wrote: > >>>>> Well, > >>>>> I changed the topology file of the system and manually typed the .itp of > >>>>> my own water model. Just a reminder that I have used my own water > >>>>> model's .itp file successfully in pure water systems. This .itp file > >>>>> starts from [ defaults ] and contains all information needed. But when > >>>>> it comes to grompp, the following error appears: > >>>>> > >>>>> Program grompp_d_mpi, VERSION 4.0.5 > >>>>> Source code file: topio.c, line: 415 > >>>>> > >>>>> Fatal error: > >>>>> Syntax error - File sixsitewater.itp, line 6 > >>>>> Last line read: > >>>>> '[ defaults ]' > >>>>> Invalid order for directive defaults > >>>>> > >>>> The only time that [defaults] should appear is in the force field that > >>>> you are > >>>> calling (i.e., ffoplsaa.itp): > >>>> > >>>> http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults > >>>> > >>>> -Justin > >>>> > >>>>> I am trying to use this water model with OPLSaa. what kind of directive > >>>>> am I missing? > >>>>> > >>>>> Payman > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote: > >>>>>> Paymon Pirzadeh wrote: > >>>>>>> Hello, > >>>>>>> I am trying to use a different water model for my proteins (using > >>>>>>> oplsaa > >>>>>>> force field). I use the .itp file which I developed, but pdb2gmx does > >>>>>>> not accept it. I am a bit confused on how I can make my water model > >>>>>>> work > >>>>>>> with OPLSaa. Based on what I saw from spc.itp or other samples, do I > >>>>>>> need to change the names of my particles in my water .itp file by > >>>>>>> including _FF_OPLS? > >>>>>> I don't know how pdb2gmx decides how to recognize water models; it may > >>>>>> be > >>>>>> hard-coded. In any case, your atom types have to be consistent with > >>>>>> OPLS > >>>>>> standards; as for whether or not you need the #ifdef _FF_OPLS in your > >>>>>> .itp file, > >>>>>> you may not need it if OPLS is the only force field with which it will > >>>>>> be used. > >>>>>> The #ifdef blocks just prevent a GROMOS system from trying to > >>>>>> recognize OPLS, etc. > >>>>>> > >>>>>> -Justin > >>>>>> > >>>>>>> Regards, > >>>>>>> > >>>>>>> Payman > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> 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/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/mailing_lists/users.php > >>>>>>> > >>> > > > > _______________________________________________ > > 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/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/mailing_lists/users.php > > > _______________________________________________ > 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/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/mailing_lists/users.php > > _______________________________________________ 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/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/mailing_lists/users.php
