[gmx-users] How to correct incomplete pdb file
Hiromichi Tsurui
tsurui at med.juntendo.ac.jp
Thu Nov 17 11:43:03 CET 2005
Hi,
Thank you Florian;
Yes, I am now using Swiss PDB viewer to correct the file.
Thank you.
Hiromichi
----- Original Message -----
From: "Florian Haberl" <Florian.Haberl at chemie.uni-erlangen.de>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, November 17, 2005 12:57 AM
Subject: Re: [gmx-users] How to correct incomplete pdb file
> 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
> --
> ---------------------------------------------------------------------------------------------------
> 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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