Hi Justin , Thank you , You are right . Problem get solved by change in spacing in PDB file. have a nice day. With Best Wishes, R.David
On Fri, Apr 6, 2012 at 6:36 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > rama david wrote: > >> HI all , >> sorry for above incomplete information , >> I change CH3 of ACE residue of my pdb file to CA . >> >> > The formatting of a .pdb file requires fixed spacing. By turning CH3 into > CA (which is correct), you deleted a space such that instead of finding > 'ACE' as the residue name, pdb2gmx is finding 'CE' since it has been > shifted to the left one space. Fix the spacing and you fix your problem. > > -Justin > > Thank you in advance >> >> >> On Fri, Apr 6, 2012 at 5:34 PM, rama david <ramadavidgr...@gmail.com<mailto: >> ramadavidgroup@gmail.**com <ramadavidgr...@gmail.com>>> wrote: >> >> Hi GROMACS Friends and Mark.. >> >> Thank you for reply ... >> My command line is >> pdb2gmx -f ....pdb -o p.pdb -p p.top -ignh -ter >> I choose the G96 53a6 ff , along with spc water model. >> >> Select start terminus type for ACE-1 >> 0: NH3+ >> 1: NH2 >> 2: None >> 2 >> Start terminus ACE-1: None >> >> Select end terminus >> 0: COO- >> 1: COOH >> 2: None >> 0 >> End terminus : COO- >> >> So I got the following out put... >> Program pdb2gmx, VERSION 4.5.4 >> Source code file: /build/buildd/gromacs-4.5.4/**src/kernel/pdb2gmx.c, >> line: 655 >> >> Fatal error: >> Atom CH3 in residue ACE 1 was not found in rtp entry ACE with 3 atoms >> while sorting atoms. >> >> . >> 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 have the limited experience for these problem.. >> Can you tell me what to do in such conditions???? >> >> I change the Atom CH3 in pdb to CA and proceed with the above >> command line >> and option . >> I got the following error >> >> Program pdb2gmx, VERSION 4.5.4 >> Source code file: /build/buildd/gromacs-4.5.4/**src/kernel/resall.c, >> line: 581 >> >> Fatal error: >> Residue 'CE' not found in residue topology database >> >> 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 have the limited experience for these problem.. >> Can you tell me what to do in such conditions???? >> >> >> On Fri, Apr 6, 2012 at 4:38 PM, Mark Abraham >> <mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.**au<mark.abra...@anu.edu.au>>> >> wrote: >> >> On 6/04/2012 9:05 PM, Mark Abraham wrote: >> >>> On 6/04/2012 8:27 PM, rama david wrote: >>> >>>> Hi Gromacs Friends and Justin , >>>> >>>> Thank you for reply and suggestion. >>>> >>>> These is short part of my PDB . >>>> >>>> ATOM 1 1H ACE 1 0.000 0.000 0.000 >>>> ATOM 2 CH3 ACE 1 0.000 1.090 0.000 >>>> ATOM 3 2H ACE 1 1.028 1.453 -0.000 >>>> ATOM 4 3H ACE 1 -0.514 1.453 -0.890 >>>> ATOM 5 C ACE 1 -0.721 1.600 1.249 >>>> ATOM 6 O ACE 1 -0.839 2.806 1.453 >>>> ATOM 7 N PRO 2 -1.227 0.727 2.126 >>>> ATOM 8 CA PRO 2 -1.918 1.181 3.321 >>>> ATOM 9 HA PRO 2 -2.553 2.031 3.073 >>>> ATOM 10 C PRO 2 -0.928 1.587 4.404 >>>> ATOM 11 O PRO 2 -1.069 2.645 5.013 >>>> ATOM 12 CB PRO 2 -2.782 0.075 3.851 >>>> ATOM 13 1HB PRO 2 -2.469 -0.177 4.864 >>>> ATOM 14 2HB PRO 2 -3.822 0.401 3.862 >>>> ATOM 15 CG PRO 2 -2.645 -1.140 2.964 >>>> ATOM 16 1HG PRO 2 -2.232 -1.966 3.542 >>>> ATOM 17 2HG PRO 2 -3.606 -1.451 2.556 >>>> ATOM 18 CD PRO 2 -1.680 -0.755 1.882 >>>> ATOM 19 1HD PRO 2 -2.173 -0.830 0.913 >>>> ATOM 20 2HD PRO 2 -0.816 -1.419 1.895 >>>> ATOM 21 N GLY 3 0.076 0.740 4.644 >>>> ATOM 22 H GLY 3 0.135 -0.114 4.109 >>>> ATOM 23 CA GLY 3 1.083 1.012 5.650 >>>> >>>> The gromacs96 53a6 .rtp file mention the following data... >>>> >>>> bondedtypes ] >>>> ; bonds angles dihedrals impropers >>>> 2 2 1 2 >>>> >>>> [ ACE ] >>>> [ atoms ] >>>> CA CH3 0.000 0 >>>> C C 0.450 1 >>>> O O -0.450 1 >>>> [ bonds ] >>>> C CA gb_27 >>>> C O gb_5 >>>> C +N gb_19 >>>> [ angles ] >>>> CA C O ga_30 CA C +N ga_19 >>>> O C +N ga_33 >>>> [ 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_9 >>>> [ angles ] >>>> -O -C N ga_33 >>>> -CA -C N ga_19 >>>> -C N H1 ga_23 >>>> -C N H2 ga_23 >>>> H1 N H2 ga_24 >>>> [ dihedrals ] >>>> -CA -C N H1 gd_14 >>>> [ impropers ] >>>> -C -O N -CA gi_1 >>>> N H1 H2 -C gi_1 >>>> As per my pdb file N atom is the part of PROLINE , not >>>> the ACE... >>>> I got the topology by using the Amber 03 FF. >>>> But my priority is to the GROMOS96 53a6 force field ... >>>> >>>> Could any suggest me the way to tackle these problem??? >>>> >>> >>> The default is to try to put termini on the protein chain. >>> Your chain already has them, so you need to tell pdb2gmx not >>> to try to add termini. See pdb2gmx -h. >>> >> >> ... and if you'd also shown the last piece of your pdb2gmx >> output and given us the whole command line you used, then you'd >> have gotten your answer faster and wasted less of people's time >> guessing what the real problem was. >> >> Mark >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<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<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> >
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