Dear Justin I got the solution. I forgot to add residue types in residuetypes.dat
Anyway thanks for your kind reply with regards, Jignesh Patel On Mon, Nov 29, 2010 at 12:17 PM, Jignesh Patel <[email protected]> wrote: > > Dear Justin, > > Thanks for your reply. > I have checked whole pdb file. Everything is fine. > > When I remove phosphorylated serine and use only serine then every thing > went fine. > > co-ordinates for phosphoserine are as per following > > ATOM 1684 N SEP X 167 27.040 22.580 8.280 1.00 > 0.00 > ATOM 1685 H SEP X 167 27.150 23.470 7.820 1.00 > 0.00 > ATOM 1686 CA SEP X 167 28.020 22.270 9.340 1.00 > 0.00 > ATOM 1687 CB SEP X 167 29.330 21.760 8.740 1.00 > 0.00 > ATOM 1688 OG SEP X 167 30.210 21.300 9.770 1.00 > 0.00 > ATOM 1689 P SEP X 167 29.763 21.418 10.657 0.80 0.00 > ATOM 1690 O1P SEP X 167 30.228 20.602 11.000 0.80 > 0.00 > ATOM 1691 O2P SEP X 167 29.298 22.234 10.314 0.80 > 0.00 > ATOM 1692 O3P SEP X 167 29.316 21.536 11.544 0.80 0.00 > ATOM 1693 C SEP X 167 28.320 23.540 10.140 1.00 > 0.00 > ATOM 1694 O SEP X 167 28.980 24.460 9.660 1.00 0.00 > > and following details regarding the error, > > Identified residue MET1 as a starting terminus. > Warning: Residue SEP167 in chain has different type (Other) from starting > residue MET1 (Protein). > Warning: Residue ASN168 in chain has different type (Protein) from starting > residue MET1 (Protein). > Warning: Residue PHE169 in chain has different type (Protein) from starting > residue MET1 (Protein). > Warning: Residue ALA170 in chain has different type (Protein) from starting > residue MET1 (Protein). > Warning: Residue VAL171 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 GLN166 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Special Atom Distance matrix: > MET1 HIS122 CYS127 MET155 HIS181 CYS232 > SD5 NE2953 SG987 SD1198 NE21417 SG1802 > HIS122 NE2953 0.896 > CYS127 SG987 2.406 2.338 > MET155 SD1198 2.631 2.424 0.726 > HIS181 NE21417 2.143 2.161 2.124 1.774 > CYS232 SG1802 2.805 3.428 3.766 3.748 2.309 > HIS273 NE22097 4.614 4.982 4.609 4.323 3.017 2.266 > Start terminus: NH3+ > End terminus: COO- > Checking for duplicate atoms.... > Now there are 283 residues with 2821 atoms > Making bonds... > Number of bonds was 2866, now 2861 > Generating angles, dihedrals and pairs... > Before cleaning: 4579 pairs > > ------------------------------------------------------- > Program pdb2gmx_d, VERSION 4.5.1 > Source code file: pgutil.c, line: 88 > > Fatal error: > Atom N not found in residue seq.nr. 1 while adding improper > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > Thanking you. > > With regards, > Jignesh Patel > > >
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