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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