Hi Justin, Thanks for the immediate response. I apologize but I don't have with me the mdp and the top files at the moment. But I will have it e-mailed once I get back to my working gromacs computer. Yes, as I remember, the [moleculetype] at the bottom of the topol.top was able to identify it as a carbohydrate. In fact, the index.file identified it as a carbohydrate. I borrowed the nvt.mdp from the Lysozyme tutorial authored by you. Thanks.
--- On Tue, 5/31/11, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Grompp error on index file To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Tuesday, May 31, 2011, 10:09 AM Mr Bernard Ramos wrote: > Hi everyone! > I added a residue on the gromacs 4.5.3 I have. I followed the instructions >as indicated in the "Adding A Residue to a Force Field" with this link >_http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_. > I added the residue to residuetypes.dat and indicated it as a carbohydrate. >The topology in fact was able to write it down as a carbohydrate. > Carbohydrates should be grouped into the "other" category; I'm not sure "Carbohydrate" is a recognized type. What do you mean the topology wrote it as a carbohydrate? Is that the [moleculetype] name it was given the topology? > __ > Generating a topology went well with pdb2gmx, editconf, genbox, energy > minimization. However, I encountered the following error when I was about to > do an NVT equilibration. > >---------------------------------------------------------------------------------------------------------------------------------- > Program grompp, VERSION 4.5.3 > Source code file: readir.c, line: 1316 > Fatal error: > Group protein not found in indexfile. > Maybe you have non-default groups in your mdp file, while not using the '-n' > option of grompp. > In that case use the '-n'option. > ---------------------------------------------------------------------------------------------------------------------------------- > In response, I created an index file using make_ndx. The index file was able >to generate correctly the molecule indices and identified it correctly as >indicated in the residuetypes.dat and carbohydrate.rtp > Your error does not appear to be connected to the carbohydrate at all. The problem appears to be the use of "protein." Capitalization shouldn't matter, so I'm not sure why grompp is complaining. > And then I tried (again) the following command: > $ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr. > It still generates the same error as above. Please help > Please provide your .mdp file and topology, if it is small enough to paste into an email. -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 ======================================== -- 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
-- 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
