Thank you very much 22 Ocak 2011 23:07 tarihinde Justin A. Lemkul <[email protected]> yazdı:
> > > ahmet yıldırım wrote: > >> please look at the attached file >> >> > I had no problem making a topology. > > $ pdb2gmx -f 3MOA.pdb -ter > > ... > Using the Gromos43a1 force field in directory gromos43a1.ff > ... > Select start terminus type for GLU-659 > 0: NH3+ > 1: NH2 > 2: None > 0 > Start terminus GLU-659: NH3+ > Select end terminus type for NH2-671 > 0: COO- > 1: COOH > 2: None > 2 > End terminus NH2-671: None > Checking for duplicate atoms.... > Now there are 13 residues with 139 atoms > Chain time... > ... > Select start terminus type for LEU-2 > 0: NH3+ > 1: NH2 > 2: None > 0 > Start terminus LEU-2: NH3+ > Select end terminus type for CYS-214 > 0: COO- > 1: COOH > 2: None > 0 > End terminus CYS-214: COO- > ... > Select start terminus type for ARG-1 > 0: NH3+ > 1: NH2 > 2: None > 0 > Start terminus ARG-1: NH3+ > Select end terminus type for ASP-217 > 0: COO- > 1: COOH > 2: None > 0 > End terminus ASP-217: COO- > ... > > -Justin > > 22 Ocak 2011 22:54 tarihinde Justin A. Lemkul <[email protected] <mailto: >> [email protected]>> yazdı: >> >> >> >> >> ahmet yıldırım wrote: >> >> 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 >> >> >> Please post your .pdb file. >> >> -Justin >> >> >> 22 Ocak 2011 00:45 tarihinde Justin A. Lemkul <[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> >> <mailto:[email protected] <mailto:[email protected]>>>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>>>> >> >> >> >> >> >> 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> <http://vt.edu> >> <http://vt.edu> | (540) >> >> 231-9080 >> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list >> [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>> >> >> >> >> 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 >> [email protected] <mailto: >> [email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>>. >> >> 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> <http://vt.edu> >> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. >> Use the www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>. >> 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> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> 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 [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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