Dear Justin, I manually specify termini. I choosed "None" but I have the same error.
Fatal error: atom C not found in residue 13NH2 while combining tdb and rtp 22 Ocak 2011 00:45 tarihinde Justin A. Lemkul <jalem...@vt.edu> yazdı: > > > ahmet yıldırım wrote: > >> Dear justin, >> >> I looked at the pdb file. No NH2 reside contains carbon atom. >> >> What should I do? >> > > In this case, you need to manually specify termini. Choose "None" to allow > your capping groups to be built properly. > > -Justin > > >> 22 Ocak 2011 00:18 tarihinde Justin A. Lemkul <jalem...@vt.edu <mailto: >> jalem...@vt.edu>> yazdı: >> >> >> >> >> ahmet yıldırım wrote: >> >> I think I need to edit the aminoacids.rtp file in gromos43a1.ff >> folder as far as I understand from mailing list. I am using 43a1 >> forcefield. I do not understand what kind of changes should I do. >> >> >> You do not need to modify the .rtp file, you need to modify your >> coordinate file, as I said before. The fatal error indicates that >> you have included a C atom in an NH2 residue, which is just a >> neutral amine and contains no carbon, as should be clear from the >> .rtp file. >> >> -Justin >> >> *the aminoacids.rtp file:* >> >> [ ACE ] >> [ atoms ] >> CA CH3 0.000 0 >> C C 0.380 1 >> O O -0.380 1 >> [ bonds ] >> C CA gb_26 >> C O gb_4 >> C +N gb_9 >> [ angles ] >> CA C O ga_30 >> CA C +N ga_18 >> O C +N ga_32 >> [ impropers ] >> C CA +N O gi_1 >> >> [ NH2 ] >> [ atoms ] >> N NT -0.83 0 >> H1 H 0.415 0 >> H2 H 0.415 0 >> [ bonds ] >> N H1 gb_2 >> N H2 gb_2 -C N gb_8 >> [ angles ] >> -O -C N ga_32 >> -CA -C N ga_18 >> -C N H1 ga_22 >> -C N H2 ga_22 >> H1 N H2 ga_23 >> [ dihedrals ] >> -CA -C N H1 gd_4 >> [ impropers ] >> -C -O N -CA gi_1 >> N H1 H2 -C gi_1 >> >> [ ALA ] >> [ atoms ] >> N N -0.28000 0 >> H H 0.28000 0 >> CA CH1 0.00000 1 >> CB CH3 0.00000 1 >> C C 0.380 2 >> O O -0.380 2 >> [ bonds ] >> N H gb_2 N CA gb_20 CA C gb_26 >> C O gb_4 C +N gb_9 CA CB gb_26 >> 2011/1/21 Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> >> <mailto:jalem...@vt.edu>>> >> >> >> >> >> ahmet yıldırım wrote: >> >> Dear users, >> >> Gromacs 4.5.3 >> pdb2gmx -f xxx.pdb -water spc >> select Force Field:9 >> *Fatal error:* >> atom C not found in buiding block 13NH2 while combining >> tdb and rtp >> For more information and tips for troubleshooting, please >> check >> the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> >> How can I fixed this error? >> >> >> You have a carbon atom in a residue that should only contain >> NH2. >> Refer to the .rtp file for what is expected, then make a >> suitable >> structure that conforms to those requirements. >> >> This has been asked and answered hundreds of times, so please >> make >> use of the mailing list search. You would have gotten your >> answer >> in minutes rather than hours. >> >> -Justin >> >> >> Thanks in advance >> >> >> -- Ahmet YILDIRIM >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- Ahmet YILDIRIM >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Ahmet YILDIRIM >> > > -- > ======================================== > > 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 > -- Ahmet YILDIRIM
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