[gmx-users] How to correct incomplete pdb file
Hiromichi Tsurui
tsurui at med.juntendo.ac.jp
Wed Nov 16 13:46:15 CET 2005
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
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