Hi Justin, Thanks for your reply, i have no particular choice i was using it for my other work and just started with it.
Now i tried it again with spc model, I still get the following error. ++++++++++++++++++++++++++++++++++++++++++++++ Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OWT3 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ++++++++++++++++++++++++++++++++++++++++++++++ I could see these atoms are defined in .itp file of gromos force filed, but i suspect some thing is going wrong with atom types in .atp file. any suggestions? Thanks Srinivs. On Fri, Jul 22, 2011 at 5:11 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > jampani srinivas wrote: > >> Hi Gromacs users, >> >> I am trying to run a fullerene simulaton in TIP4P water model, i am using >> the "c70_G53a6.itp <http://tfy.tkk.fi/soft/** >> downloads/files/c70_G53a6.itp<http://tfy.tkk.fi/soft/downloads/files/c70_G53a6.itp> >> >**" file downloaded from >> >http://tfy.tkk.fi/soft/**downloads/<http://tfy.tkk.fi/soft/downloads/>. >> i have added TIP4P water model using genbox command, later when i am trying >> to generate .tpr file for energy minimization it gives me the following >> error. >> ------------------------------**------------------------- >> Program grompp, VERSION 4.5.4 >> Source code file: toppush.c, line: 1166 >> >> Fatal error: >> Atomtype OWT4 not found >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at >> http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> >> ------------------------------**------------------------- >> >> I looked up in the mailing list and found many helpful comments but i >> could not resolve the problem, i searched in the tip4p.itp file of gromos >> force field and i could see that tip4p water model is defined in that file, >> but i could not find the atom types defined in atomtypes.atp file. when i >> try to enter the atom types for some reason it does not read my entries. >> > > This may or may not be related to a bug that has been fixed in the > development version of the code. Simply adding OWT4 into atomtypes.atp is > insufficient; you need to add nonbonded parameters in ffnonbonded.itp as > well. Without seeing the actual error message(s) you're getting, I don't > dare guess further. > > here is my .top file >> >> ; The force field files to be included >> >> #include "ffG53a6.itp" >> >> [ moleculetype ] >> #include "fullerene.itp" >> >> ; Include water topology >> #include "tip4p.itp" >> >> [ system ] >> Fullerene in Water >> >> [ molecule ] >> FUL 1 >> SOL 1696 >> >> Can anybody help me? >> >> > Is there a particular reason you need to use TIP4P? The Gromos force > fields were parameterized with SPC water, so that's what is expected to > work. In principle, you should be able to use any water model you want, but > you still have to demonstrate that it's a valid approach. > > -Justin > > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- ********************************************* *J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics, Drexel University 3141 Chestnut St, Philadelphia, PA 19104 Ph: 215-895-1989 Web:http://jsrao.web.officelive.com/default.aspx* **********************************************
-- 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
