[gmx-users] How to correct incomplete pdb file

[Florian Haberl]

Hi,

you can try "pdb2gmx -ignh" as option, all hydogen atoms will be ignored.

Or take a look with your favorite pdb viewer (like swissprot pdb viewer) on 
your protein.

On Wednesday 16 November 2005 13:46, Hiromichi Tsurui wrote:
> Hi, all of Gromacs users;
>
> I tried to generate topology file for a pdb (1IAO.pdb) using pdb2gmx with
> the option -missing.
> pdb2gmx showed alarm shown below;
> It seems some information about His15 of B chain is incomplete.
> Does any one let me know how to correct such defect in pdb file ?
>
> Thank you.
>
> ###########################################################################
>################ Opening library file
> /usr/local/gromacs/share/top/FF.dat2Opening library file
> /usr/local/gromacs/share/top/ffG43a2.rtpOpening library file
> /usr/local/gromacs/share/top/aminoacids.datOpening library file
> /usr/local/gromacs/share/top/xlateat.dat23 out of 23 lines of xlateat.dat
> converted succesfullyAll occupancies are oneOpening library file
> /usr/local/gromacs/share/top/ffG43a2.atpAtomtype 50Opening library file
> /usr/local/gromacs/share/top/ffG43a2.rtpResidue 96Sorting it all
> out...Opening library file /usr/local/gromacs/share/top/ffG43a2.hdbOpening
> library file /usr/local/gromacs/share/top/ffG43a2-n.tdbOpening library file
> /usr/local/gromacs/share/top/ffG43a2-c.tdb Back Off! I just backed up
> 1IAO.top to ./#1IAO.top.4#Opening library file
> /usr/local/gromacs/share/top/specbond.dat5 out of 5 lines of specbond.dat
> converted succesfullySpecial Atom Distance matrix:                    HIS4
> HIS24   HIS68  CYS107  HIS143  HIS146  CYS163                   NE232
> NE2187  NE2548   SG839 NE21129 NE21156  SG1287   HIS24  NE2187   1.679
> HIS68  NE2548   3.616   2.167  CYS107   SG839   2.903   2.749   3.792
> HIS143 NE21129   2.339   1.813   2.066   2.440  HIS146 NE21156   1.838
> 1.721   3.025   1.224   1.484  CYS163  SG1287   3.074   2.837   3.810
> 0.203   2.544   1.376  HIS167 NE21322   3.326   2.681   2.823   1.439
> 1.707   1.557   1.417  HIS177 NE21403   3.949   3.833   4.636   1.103
> 3.329   2.294   1.000                  HIS167                 NE21322
> HIS177 NE21403   1.945Linking CYS-107 SG-839 and CYS-163 SG-1287...There
> are 261 donors and 264 acceptorsThere are 413 hydrogen bondsWill use HISB
> for residue 4Will use HISA for residue 24Will use HISB for residue 68Will
> use HISB for residue 143Will use HISA for residue 146Will use HISB for
> residue 167Will use HISB for residue 177 Back Off! I just backed up
> 1IAO_A.itp to ./#1IAO_A.itp.4#Making bonds...Opening library file
> /usr/local/gromacs/share/top/aminoacids.dat WARNING: atom CG1 is missing in
> residue ILE 52 in the pdb file  WARNING: atom CG2 is missing in residue ILE
> 52 in the pdb file  WARNING: atom CD is missing in residue ILE 52 in the
> pdb file  WARNING: atom CB is missing in residue SER 125 in the pdb file
> WARNING: atom OG is missing in residue SER 125 in the pdb file  WARNING:
> atom HG is missing in residue SER 125 in the pdb file         You might
> need to add atom HG to the hydrogen database of residue SER         in the
> file ff???.hdb (see the manual)  WARNING: atom CB is missing in residue
> LYSH 126 in the pdb file  WARNING: atom CG is missing in residue LYSH 126
> in the pdb file  WARNING: atom CD is missing in residue LYSH 126 in the pdb
> file WARNING: atom CE is missing in residue LYSH 126 in the pdb file 
> WARNING: atom NZ is missing in residue LYSH 126 in the pdb file  WARNING:
> atom HZ1 is missing in residue LYSH 126 in the pdb file         You might
> need to add atom HZ1 to the hydrogen database of residue LYSH         in
> the file ff???.hdb (see the manual)  WARNING: atom HZ2 is missing in
> residue LYSH 126 in the pdb file         You might need to add atom HZ2 to
> the hydrogen database of residue LYSH         in the file ff???.hdb (see
> the manual) WARNING: atom HZ3 is missing in residue LYSH 126 in the pdb
> file         You might need to add atom HZ3 to the hydrogen database of
> residue LYSH in the file ff???.hdb (see the manual)  WARNING: atom CG is
> missing in residue ASP 158 in the pdb file  WARNING: atom OD1 is missing in
> residue ASP 158 in the pdb file  WARNING: atom OD2 is missing in residue
> ASP 158 in the pdb file  WARNING: atom CG is missing in residue ASP 159 in
> the pdb file WARNING: atom OD1 is missing in residue ASP 159 in the pdb
> file  WARNING: atom OD2 is missing in residue ASP 159 in the pdb file 
> WARNING: atom CG1 is missing in residue ILE 160 in the pdb file  WARNING:
> atom CG2 is missing in residue ILE 160 in the pdb file  WARNING: atom CG is
> missing in residue GLU 172 in the pdb file  WARNING: atom CD is missing in
> residue GLU 172 in the pdb file  WARNING: atom OE1 is missing in residue
> GLU 172 in the pdb file WARNING: atom OE2 is missing in residue GLU 172 in
> the pdb file There were 27 missing atoms in molecule Protein_ANumber of
> bonds was 1863, now 1858Generating angles, dihedrals and pairs...Before
> cleaning: 2874 pairsBefore cleaning: 3615 dihedralsThere are  938
> dihedrals,  996 impropers, 2737 angles          2874 pairs,     1858 bonds
> and     0 dummiesTotal mass 19952.404 a.m.u.Total charge -8.000 eWriting
> topology Back Off! I just backed up posre_A.itp to ./#posre_A.itp.3#Opening
> library file /usr/local/gromacs/share/top/specbond.dat5 out of 5 lines of
> specbond.dat converted succesfullySpecial Atom Distance matrix:            
>        HIS8 HIS11   CYS24   CYS88   HIS90  HIS121  HIS122                  
> NE254 NE274   SG174   SG717  NE2738  NE2963  NE2973   HIS11   NE274   0.684
> CYS24   SG174   1.625   2.158   CYS88   SG717   1.508   2.078   0.201 HIS90
>  NE2738   1.654   2.301   1.259   1.074  HIS121  NE2963   6.383 6.562  
> 5.183   5.337   5.894  HIS122  NE2973   6.178   6.411   4.907 5.054   5.561
>   0.567  CYS127  SG1009   4.918   5.244   3.703   3.798 4.037   2.288  
> 1.853  HIS176 NE21411   7.211   7.510   5.900   6.021 6.339   1.797   1.485
>  CYS183  SG1460   4.965   5.309   3.701   3.799 4.047   2.298   1.832 
> HIS184 NE21470   4.969   5.412   3.556   3.645 3.833   2.933   2.401 
> HIS187 NE21496   3.736   4.166   2.468   2.533 2.675   3.464   3.048       
>           CYS127  HIS176  CYS183  HIS184 SG1009 NE21411  SG1460 NE21470 
> HIS176 NE21411   2.360  CYS183  SG1460 0.203   2.308  HIS184 NE21470  
> 1.116   2.669   0.935  HIS187 NE21496 1.398   3.668   1.382   1.300Linking
> CYS-24 SG-174 and CYS-88
> SG-717...Linking CYS-127 SG-1009 and CYS-183 SG-1460...There are 326 donors
> and 307 acceptorsThere are 456 hydrogen bondsWill use HISB for residue
> 8Will use HISB for residue 11Fatal error: Incomplete ring in HIS15
>
> Hiromichi Tsurui MD, PhD
> Dept. Pathology,
> Juntendo University
> Phone:81-3-5802-1039
> Fax:81-3-3813-3164
> tsurui at med.juntendo.ac.jp


Greetings,

Florian
-- 
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 Florian Haberl                             Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
 
 Mailto: florian.haberl AT chemie.uni-erlangen.de
 
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