<br>Dear Justin<br><br>I got the solution. I forgot to add residue types in residuetypes.dat<br><br>Anyway thanks for your kind reply<br><br><br>with regards,<br>Jignesh Patel<br><br><br><div class="gmail_quote">On Mon, Nov 29, 2010 at 12:17 PM, Jignesh Patel <span dir="ltr"><<a href="mailto:jbp087@gmail.com">jbp087@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>Dear Justin,<br><br>Thanks for your reply.<br>I have checked whole pdb file. Everything is fine.<br>
<br>When I remove phosphorylated serine and use only serine then every thing went fine.<br><br>co-ordinates for phosphoserine are as per following<br>
<br>ATOM 1684 N SEP X 167 27.040 22.580 8.280 1.00 0.00 <br>ATOM 1685 H SEP X 167 27.150 23.470 7.820 1.00 0.00 <br>ATOM 1686 CA SEP X 167 28.020 22.270 9.340 1.00 0.00 <br>
ATOM 1687 CB SEP X 167 29.330 21.760 8.740 1.00 0.00 <br>ATOM 1688 OG SEP X 167 30.210 21.300 9.770 1.00 0.00 <br>ATOM 1689 P SEP X 167 29.763 21.418 10.657 0.80 0.00<br>
ATOM 1690 O1P SEP X 167 30.228 20.602 11.000 0.80 0.00 <br>ATOM 1691 O2P SEP X 167 29.298 22.234 10.314 0.80 0.00 <br>ATOM 1692 O3P SEP X 167 29.316 21.536 11.544 0.80 0.00 <br>
ATOM 1693 C SEP X 167 28.320 23.540 10.140 1.00 0.00 <br>ATOM 1694 O SEP X 167 28.980 24.460 9.660 1.00 0.00 <br><br>and following details regarding the error,<br><br>Identified residue MET1 as a starting terminus.<br>
Warning: Residue SEP167 in chain has different type (Other) from starting residue MET1 (Protein).<br>Warning: Residue ASN168 in chain has different type (Protein) from starting residue MET1 (Protein).<br>Warning: Residue PHE169 in chain has different type (Protein) from starting residue MET1 (Protein).<br>
Warning: Residue ALA170 in chain has different type (Protein) from starting residue MET1 (Protein).<br>Warning: Residue VAL171 in chain has different type (Protein) from starting residue MET1 (Protein).<br>More than 5 unidentified residues at end of chain - disabling further warnings.<br>
Identified residue GLN166 as a ending terminus.<br>8 out of 8 lines of specbond.dat converted successfully<br>Special Atom Distance matrix:<br> MET1 HIS122 CYS127 MET155 HIS181 CYS232<br> SD5 NE2953 SG987 SD1198 NE21417 SG1802<br>
HIS122 NE2953 0.896<br> CYS127 SG987 2.406 2.338<br> MET155 SD1198 2.631 2.424 0.726<br> HIS181 NE21417 2.143 2.161 2.124 1.774<br> CYS232 SG1802 2.805 3.428 3.766 3.748 2.309<br>
HIS273 NE22097 4.614 4.982 4.609 4.323 3.017 2.266<br>
Start terminus: NH3+<br>End terminus: COO-<br>Checking for duplicate atoms....<br>Now there are 283 residues with 2821 atoms<br>Making bonds...<br>Number of bonds was 2866, now 2861<br>Generating angles, dihedrals and pairs...<br>
Before cleaning: 4579 pairs<br><br>-------------------------------------------------------<br>Program pdb2gmx_d, VERSION 4.5.1<br>Source code file: pgutil.c, line: 88<br><br>Fatal error:<br>Atom N not found in residue <a href="http://seq.nr" target="_blank">seq.nr</a>. 1 while adding improper<br>
<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br>
<br>Thanking you.<br><br>With regards,<br>Jignesh Patel<br><br><br></blockquote></div><br>