On Sat, Jul 6, 2013 at 4:30 PM, Albert <mailmd2...@gmail.com> wrote: > On 07/06/2013 12:14 PM, Mark Abraham wrote: >> >> My bad. Use >> >> warning_note(wi, "Debugging"); > > > > thanks a lot Mark. I've obtained some informations now:
That's a completely different output. I think both your executables are broken, somehow. Clean the build and install trees and try again :-) Mark > Identified residue MET1 as a starting terminus. > Warning: Residue RETK296 in chain has different type (Other) from starting > residue MET1 (Protein). > Warning: Residue THR297 in chain has different type (Protein) from starting > residue MET1 (Protein). > Warning: Residue SER298 in chain has different type (Protein) from starting > residue MET1 (Protein). > Warning: Residue ALA299 in chain has different type (Protein) from starting > residue MET1 (Protein). > Warning: Residue VAL300 in chain has different type (Protein) from starting > residue MET1 (Protein). > More than 5 unidentified residues at end of chain - disabling further > warnings. > Identified residue ALA295 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Special Atom Distance matrix: > Fatal error: > Residue 1 named LEU of a molecule in the input file was mapped > to an entry in the topology database, but the atom N used in > an interaction of type improper in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > "History has expired" (PubMed Central) > > > > I take 11-cis-retinal SCHIFF base charmm format topology from the > publication (Biophysical Journal, 83:3097-3112, 2002) from here: > > http://www.ks.uiuc.edu/Research/namd/wiki/?ParameterTopologyRepository > > and convert into gromacs .itp format: > > ; PROTONATED SCHIFF BASE > [ RETK ] > [ atoms ] > N NH1 -0.47000 0 > HN H 0.31000 1 > CA CT1 0.07000 2 > HA HB 0.09000 3 > C C 0.51000 4 > O O -0.51000 5 > CB CT2 -0.18000 6 > HB1 HA 0.09000 7 > HB2 HA 0.09000 8 > CG CT2 -0.18000 9 > HG1 HA 0.09000 10 > HG2 HA 0.09000 11 > CD CT2 -0.18000 12 > HD1 HA 0.09000 13 > HD2 HA 0.09000 14 > CE CT2 0.340 15 > HE1 HA 0.050 16 > HE2 HA 0.050 17 > N16 NCH1 -0.727 18 > H16 HCR 0.505 19 > C15 CR15 0.362 20 > H15 HPL1 0.189 21 > C14 CR14 -0.180 22 > H14 HPL 0.180 23 > C13 CR13 0.131 24 > C20 CT3 -0.170 25 > H20A HA 0.090 26 > H20B HA 0.090 27 > H20C HA 0.090 28 > C12 CR12 -0.110 29 > H12 HPL 0.110 30 > C11 CR11 -0.090 31 > H11 HPL 0.090 32 > C10 CR10 -0.100 33 > H10 HPL 0.100 34 > C9 CR9 0.00 35 > C19 CT3 -0.27 36 > H19A HA 0.09 37 > H19B HA 0.09 38 > H19C HA 0.09 39 > C8 CR8 -0.10 40 > H8 HPL 0.10 41 > C7 CR7 -0.10 42 > H7 HPL 0.10 43 > C6 CR6 0.00 44 > C5 CR5 0.00 45 > C18 CT3 -0.27 46 > H18A HA 0.09 47 > H18B HA 0.09 48 > H18C HA 0.09 49 > C4 CT2 -0.20 50 > H4A HA 0.10 51 > H4B HA 0.10 52 > C3 CT2 -0.20 53 > H3A HA 0.10 54 > H3B HA 0.10 55 > C2 CT2 -0.20 56 > H2A HA 0.10 57 > H2B HA 0.10 58 > C1 CT3 0.00 59 > C16 CT3 -0.27 60 > H16A HA 0.09 61 > H16B HA 0.09 62 > H16C HA 0.09 63 > C17 CT3 -0.27 64 > H17A HA 0.09 65 > H17B HA 0.09 66 > H17C HA 0.09 67 > > [ bonds ] > CB CA > CG CB > CD CG > CE CD > N16 CE > N HN > N CA > O C > > C CA > C +N > CA HA > CB HB1 > CB HB2 > CG HG1 > CG HG2 > CD HD1 > CD HD2 > CE HE1 > CE HE2 > C1 C2 > C1 C6 > C1 C16 > C1 C17 > C2 C3 > C2 H2A > C2 H2B > C3 C4 > C3 H3A > C3 H3B > C4 C5 > C4 H4A > C4 H4B > > C5 C6 > C5 C18 > C6 C7 > C7 C8 > C7 H7 > C8 C9 > C8 H8 > C9 C10 > C9 C19 > C10 C11 > C10 H10 > C11 C12 > C11 H11 > C12 C13 > C12 H12 > C13 C14 > C13 C20 > C14 C15 > C14 H14 > C15 N16 > C15 H15 > N16 H16 > C16 H16A > C16 H16B > C16 H16C > C17 H17A > C17 H17B > C17 H17C > C18 H18A > C18 H18B > C18 H18C > C19 H19A > C19 H19B > C19 H19C > C20 H20A > C20 H20B > C20 H20C > > [ impropers ] > N -C CA HN > C CA +N O > C5 C6 C4 C18 > C6 C1 C5 C7 > C7 C8 C6 H7 > C8 C7 C9 H8 > C9 C10 C8 C19 > C10 C9 C11 H10 > C11 C12 C10 H11 > C12 C11 C13 H12 > C13 C14 C12 C20 > C14 C13 C15 H14 > C15 N16 C14 H15 > N16 CE C15 H16 > > Then I add this information into the aminoacide.rtp file. I don't know why > it failed. It is expected to be treated as regular amino acid residue.... > > thank you very much. > > > Albert > -- > 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 -- 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
