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)?
Payman 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
