HI all , sorry for above incomplete information , I change CH3 of ACE residue of my pdb file to CA .
Thank you in advance On Fri, Apr 6, 2012 at 5:34 PM, rama david <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 > ------------------------------------------------------- > 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 > ------------------------------------------------------- > 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>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 >> 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 >> > >
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