Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any other information. I followed your suggestions and able to generate a biphasic system of water/octane containing a protein molecule. But, when I tried grompp on this biphasic system (containing octane+water+protein), it results in error even if I include the topologies in forcefield.itp file.
The error was Fatal error: Atomtype hc not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bipin singh wrote: >> >> Thanks for your reply. >> But as far as I understood, in order to use these GAFF topology (for >> e.g. to perform simulation using these topologies) with Gromacs we >> have to incorporate the information from these topologies to the >> existing Amber forcefields in Gromacs or Is there anyway (Possibility >> of using Standalone GAFF parameters in Gromacs) to do it without >> performing this task. >> > > As David said, the topologies stand on their own. You do not need to call > any further information from anywhere. The .top that you downloaded begins > with a [defaults] directive, declares atom types, and proceeds through the > rest of the topology with explicit parameters. > > >> As you said these topologies are self supporting and we do not need to >> change ffbonded.itp, but during grompp I got the following error, may >> be because I have not added the dihedral information. >> >> ERROR [file oct.top]: >> No default Proper Dih. types >> >> Please provide your suggestions. >> > > I certainly don't see how this could have happened. All the dihedral > parameters are listed explicitly. The fatal error should have printed a > line number in the .top that is problematic, so start by investigating > there. If you have modified the topology in any way, then undo the changes > and try again. > > I did not have any trouble using this .top in an unmodified form, so I > suspect you've altered it in some way that has broken it. > > -Justin > > >> >> On Mon, Mar 26, 2012 at 17:29, David van der Spoel <sp...@xray.bmc.uu.se> >> wrote: >>> >>> On 2012-03-26 13:55, bipin singh wrote: >>>> >>>> Hello all, >>>> >>>> I am using the GAFF topology provided for octan-1-ol at Gromacs liquid >>>> database (http://virtualchemistry.org/molecules/111-87-5/index.php). I >>>> have incorporated all the parameters >>>> for atoms, bonds and non-bonded interaction type in the forcefield >>>> (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I >>>> am not sure how to add the dihedraltypes information in ffbonded.itp >>>> from the GAFF topology as to add this information I need the phase and >>>> kd for each dihedral. Is this information is available in the GAFF >>>> topology provided in the Gromacs database ? >>>> >>>> >>> This topology is self supporting and you do not need anything else in >>> ffbonded.itp. >>> >>> You should be careful merging such parameters with an existing force >>> field, >>> because strictly speaking these are different force fields. >>>> >>>> >>>> >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >>> -- >>> 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 >> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 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 -- ----------------------- Regards, Bipin Singh -- 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
