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<DIV><FONT face="MS UI Gothic">Hi, all of Gromacs users;</FONT></DIV>
<DIV><FONT face="MS UI Gothic"></FONT> </DIV>
<DIV><FONT face="MS UI Gothic">I tried to generate topology file for a pdb
(1IAO.pdb) using pdb2gmx with the option -missing.</FONT></DIV>
<DIV><FONT face="MS UI Gothic">pdb2gmx showed alarm shown below;</FONT></DIV>
<DIV><FONT face="MS UI Gothic">It seems some information about His15 of B chain
is incomplete.</FONT></DIV>
<DIV><FONT face="MS UI Gothic">Does any one let me know how to correct such
defect in pdb file ?</FONT></DIV>
<DIV><FONT face="MS UI Gothic"></FONT> </DIV>
<DIV><FONT face="MS UI Gothic">Thank you.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face="MS UI Gothic"
size=2>###########################################################################################</FONT></DIV><PRE><FONT face="Cumberland, monospace">Opening library file /usr/local/gromacs/share/top/FF.dat<BR>2<BR>Opening library file /usr/local/gromacs/share/top/ffG43a2.rtp<BR>Opening library file /usr/local/gromacs/share/top/aminoacids.dat<BR>Opening library file /usr/local/gromacs/share/top/xlateat.dat<BR>23 out of 23 lines of xlateat.dat converted succesfully<BR>All occupancies are one<BR>Opening library file /usr/local/gromacs/share/top/ffG43a2.atp<BR>Atomtype 50<BR>Opening library file /usr/local/gromacs/share/top/ffG43a2.rtp<BR>Residue 96<BR>Sorting it all out...<BR>Opening library file /usr/local/gromacs/share/top/ffG43a2.hdb<BR>Opening library file /usr/local/gromacs/share/top/ffG43a2-n.tdb<BR>Opening library file /usr/local/gromacs/share/top/ffG43a2-c.tdb<BR> <BR>Back Off! I just backed up 1IAO.top to ./#1IAO.top.4#<BR>Opening library file /usr/local/gromacs/share/top/specbond.dat<BR>5 out of 5 lines of specbond.dat converted succesfully<BR>Special Atom Distance matrix:<BR> HIS4 HIS24 HIS68 CYS107 HIS143 HIS146 CYS163<BR> NE232 NE2187 NE2548 SG839 NE21129 NE21156 SG1287<BR> HIS24 NE2187 1.679<BR> HIS68 NE2548 3.616 2.167<BR> CYS107 SG839 2.903 2.749 3.792<BR> HIS143 NE21129 2.339 1.813 2.066 2.440<BR> HIS146 NE21156 1.838 1.721 3.025 1.224 1.484<BR> CYS163 SG1287 3.074 2.837 3.810 0.203 2.544 1.376<BR> HIS167 NE21322 3.326 2.681 2.823 1.439 1.707 1.557 1.417<BR> HIS177 NE21403 3.949 3.833 4.636 1.103 3.329 2.294 1.000<BR> HIS167<BR> NE21322<BR> HIS177 NE21403 1.945<BR>Linking CYS-107 SG-839 and CYS-163 SG-1287...<BR>There are 261 donors and 264 acceptors<BR>There are 413 hydrogen bonds<BR>Will use HISB for residue 4<BR>Will use HISA for residue 24<BR>Will use HISB for residue 68<BR>Will use HISB for residue 143<BR>Will use HISA for residue 146<BR>Will use HISB for residue 167<BR>Will use HISB for residue 177<BR> <BR>Back Off! I just backed up 1IAO_A.itp to ./#1IAO_A.itp.4#<BR>Making bonds...<BR>Opening library file /usr/local/gromacs/share/top/aminoacids.dat<BR> <BR>WARNING: atom CG1 is missing in residue ILE 52 in the pdb file<BR> <BR> <BR>WARNING: atom CG2 is missing in residue ILE 52 in the pdb file<BR> <BR> <BR>WARNING: atom CD is missing in residue ILE 52 in the pdb file<BR> <BR> <BR>WARNING: atom CB is missing in residue SER 125 in the pdb file<BR> <BR> <BR>WARNING: atom OG is missing in residue SER 125 in the pdb file<BR> <BR> <BR>WARNING: atom HG is missing in residue SER 125 in the pdb file<BR> You might need to add atom HG to the hydrogen database of residue SER<BR> in the file ff???.hdb (see the manual)<BR> <BR> <BR>WARNING: atom CB is missing in residue LYSH 126 in the pdb file<BR> <BR> <BR>WARNING: atom CG is missing in residue LYSH 126 in the pdb file<BR> <BR> <BR>WARNING: atom CD is missing in residue LYSH 126 in the pdb file<BR> <BR> <BR>WARNING: atom CE is missing in residue LYSH 126 in the pdb file<BR> <BR> <BR>WARNING: atom NZ is missing in residue LYSH 126 in the pdb file<BR> <BR> <BR>WARNING: atom HZ1 is missing in residue LYSH 126 in the pdb file<BR> You might need to add atom HZ1 to the hydrogen database of residue LYSH<BR> in the file ff???.hdb (see the manual)<BR> <BR> <BR>WARNING: atom HZ2 is missing in residue LYSH 126 in the pdb file<BR> You might need to add atom HZ2 to the hydrogen database of residue LYSH<BR> in the file ff???.hdb (see the manual)<BR> <BR> <BR>WARNING: atom HZ3 is missing in residue LYSH 126 in the pdb file<BR> You might need to add atom HZ3 to the hydrogen database of residue LYSH<BR> in the file ff???.hdb (see the manual)<BR> <BR> <BR>WARNING: atom CG is missing in residue ASP 158 in the pdb file<BR> <BR> <BR>WARNING: atom OD1 is missing in residue ASP 158 in the pdb file<BR> <BR> <BR>WARNING: atom OD2 is missing in residue ASP 158 in the pdb file<BR> <BR> <BR>WARNING: atom CG is missing in residue ASP 159 in the pdb file<BR> <BR> <BR>WARNING: atom OD1 is missing in residue ASP 159 in the pdb file<BR> <BR> <BR>WARNING: atom OD2 is missing in residue ASP 159 in the pdb file<BR> <BR> <BR>WARNING: atom CG1 is missing in residue ILE 160 in the pdb file<BR> <BR> <BR>WARNING: atom CG2 is missing in residue ILE 160 in the pdb file<BR> <BR> <BR>WARNING: atom CG is missing in residue GLU 172 in the pdb file<BR> <BR> <BR>WARNING: atom CD is missing in residue GLU 172 in the pdb file<BR> <BR> <BR>WARNING: atom OE1 is missing in residue GLU 172 in the pdb file<BR> <BR> <BR>WARNING: atom OE2 is missing in residue GLU 172 in the pdb file<BR> <BR>There were 27 missing atoms in molecule Protein_A<BR>Number of bonds was 1863, now 1858<BR>Generating angles, dihedrals and pairs...<BR>Before cleaning: 2874 pairs<BR>Before cleaning: 3615 dihedrals<BR>There are 938 dihedrals, 996 impropers, 2737 angles<BR> 2874 pairs, 1858 bonds and 0 dummies<BR>Total mass 19952.404 a.m.u.<BR>Total charge -8.000 e<BR>Writing topology<BR> <BR>Back Off! I just backed up posre_A.itp to ./#posre_A.itp.3#<BR>Opening library file /usr/local/gromacs/share/top/specbond.dat<BR>5 out of 5 lines of specbond.dat converted succesfully<BR>Special Atom Distance matrix:<BR> HIS8 HIS11 CYS24 CYS88 HIS90 HIS121 HIS122<BR> NE254 NE274 SG174 SG717 NE2738 NE2963 NE2973<BR> HIS11 NE274 0.684<BR> CYS24 SG174 1.625 2.158<BR> CYS88 SG717 1.508 2.078 0.201<BR> HIS90 NE2738 1.654 2.301 1.259 1.074<BR> HIS121 NE2963 6.383 6.562 5.183 5.337 5.894<BR> HIS122 NE2973 6.178 6.411 4.907 5.054 5.561 0.567<BR> CYS127 SG1009 4.918 5.244 3.703 3.798 4.037 2.288 1.853<BR> HIS176 NE21411 7.211 7.510 5.900 6.021 6.339 1.797 1.485<BR> CYS183 SG1460 4.965 5.309 3.701 3.799 4.047 2.298 1.832<BR> HIS184 NE21470 4.969 5.412 3.556 3.645 3.833 2.933 2.401<BR> HIS187 NE21496 3.736 4.166 2.468 2.533 2.675 3.464 3.048<BR> CYS127 HIS176 CYS183 HIS184<BR> SG1009 NE21411 SG1460 NE21470<BR> HIS176 NE21411 2.360<BR> CYS183 SG1460 0.203 2.308<BR> HIS184 NE21470 1.116 2.669 0.935<BR> HIS187 NE21496 1.398 3.668 1.382 1.300<BR>Linking CYS-24 SG-174 and CYS-88 SG-717...<BR>Linking CYS-127 SG-1009 and CYS-183 SG-1460...<BR>There are 326 donors and 307 acceptors<BR>There are 456 hydrogen bonds<BR>Will use HISB for residue 8<BR>Will use HISB for residue 11<BR>Fatal error: Incomplete ring in HIS15<BR></FONT></PRE>
<DIV><FONT face="MS UI Gothic"></FONT> </DIV>
<DIV><FONT face="MS UI Gothic"></FONT> </DIV>
<DIV><FONT face="MS UI Gothic" size=2>Hiromichi Tsurui MD, PhD<BR>Dept.
Pathology, <BR>Juntendo
University<BR>Phone:81-3-5802-1039<BR>Fax:81-3-3813-3164<BR><A
href="mailto:tsurui@med.juntendo.ac.jp">tsurui@med.juntendo.ac.jp</A></FONT></DIV></BODY></HTML>