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Hi everybody,<br><br>My problem is the following: I am studying the chromosome partitioning protein ParB from Burkholderia <span class="ecxhighlight" style="">cenocepacia</span> J2315. As no crystal structure was available, I used I-TASSER to predict its 3d structure.<br><br>In
order to refine the structure, I am now using in Gromacs the pdb file
I've obtained, following the Lysozime tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html.<br><br>The
problem is that after running pdb2gmx the protein has a net charge of
-4.68, which indicates that a problem has ocurred, but pdb2gmx doesn't
seem to be presenting any critical error message.<br><br>PDB file: http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S64445/<br><br>Best regards,<br><br>Marcelo<br><br>------------------------------------------------------------------------<br><br>pdb2gmx output:<br><br>Opening library file /usr/share/gromacs/top/ffoplsaa.rtp<br>Opening library file /usr/share/gromacs/top/aminoacids.dat<br>Opening library file /usr/share/gromacs/top/aminoacids.dat<br>WARNING: masses will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /usr/share/gromacs/top/atommass.dat<br>Entries in atommass.dat: 178<br>WARNING: vdwradii will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /usr/share/gromacs/top/vdwradii.dat<br>Entries in vdwradii.dat: 28<
br>Opening library file /usr/share/gromacs/top/dgsolv.dat<br>Entries in dgsolv.dat: 7<br>Opening library file /usr/share/gromacs/top/electroneg.dat<br>Entries in electroneg.dat: 71<br>Opening library file /usr/share/gromacs/top/elements.dat<br>Entries in elements.dat: 218<br>Reading prot.pdb...<br>Read 'protein', 4573 atoms<br>Opening library file /usr/share/gromacs/top/xlateat.dat<br>26 out of 26 lines of xlateat.dat converted succesfully<br>Analyzing pdb file<br>There are 1 chains and 0 blocks of water and 297 residues with 4573 atoms<br><br> chain #res #atoms<br> 1 'A' 297 4573 <br><br>All occupancies are one<br>Opening library file /usr/share/gromacs/top/ffoplsaa.atp<br>Atomtype 1<br>Reading residue database... (ffoplsaa)<br>Opening library file /usr/share/gromacs/top/ffoplsaa.rtp<br>Residue 59<br>Sorting it all out...<br>Opening library file /usr/share/gromacs/top/ffoplsaa.hdb<br>Opening library file /usr/share/gromacs/top
/ffoplsaa-n.tdb<br>Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb<br><br>Back Off! I just backed up topol.top to ./#topol.top.7#<br>Processing chain 1 'A' (4573 atoms, 297 residues)<br>There are 451 donors and 430 acceptors<br>There are 670 hydrogen bonds<br>Will use HISB for residue 137<br>Will use HISB for residue 150<br>Will use HISB for residue 190<br>Will use HISB for residue 207<br>Will use HISB for residue 225<br>Checking for duplicate atoms....<br>Opening library file /usr/share/gromacs/top/specbond.dat<br>7 out of 7 lines of specbond.dat converted succesfully<br>Special Atom Distance matrix:<br> MET1 MET53 MET71 MET119 HISB137 HISB150 MET180<br> SD10 SD795 SD1051 SD1801 N
E22091 NE22301 SD2752<br> MET53 SD795 2.734<br> MET71 SD1051 3.599 1.900<br> MET119 SD1801 3.866 2.738 1.752<br> HISB137 NE22091 3.420 2.337 2.726 1.784<br> HISB150 NE22301 3.300 3.399 3.547 2.251 1.488<br> MET180 SD2752 2.714 2.430 3.872 3.588 2.019 2.534<br> MET188 SD2867 1.831 2.554 3.389 2.903 1.893 1.645 1.520<br> HISB190 NE22894 1.854 2.621 3.979 3.803 2.535 2.621 1.015<br> HISB207 NE23144 3.293 3.005 4.536
4.229 2.555 3.052 0.734<br> MET214 SD3267 2.343 3.284 4.746 4.546 3.162 3.163 1.349<br> HISB225 NE23449 3.197 4.310 5.713 5.308 3.829 3.582 2.113<br> MET188 HISB190 HISB207 MET214<br> SD2867 NE22894 NE23144 SD3267<br> HISB190 NE22894 1.112<br> HISB207 NE23144 2.169 1.485<br> MET214 SD3267 1.790 0.783 1.422<br> HISB225 NE23449 2.522 1.762 1.900 1.063<br>N-terminus: NH3+<br>C-terminus: COO-<br>Now there
are 297 residues with 4577 atoms<br>Making bonds...<br>Opening library file /usr/share/gromacs/top/aminoacids.dat<br>Number of bonds was 4596, now 4596<br>Generating angles, dihedrals and pairs...<br>Before cleaning: 12035 pairs<br>Before cleaning: 12105 dihedrals<br>Keeping all generated dihedrals<br>There are 12105 dihedrals, 838 impropers, 8351 angles<br> 12017 pairs, 4596 bonds and 0 virtual sites<br>Total mass 32038.885 a.m.u.<br>Total charge -4.680 e<br>Writing topology<br><br>Back Off! I just backed up posre.itp to ./#posre.itp.4#<br><br>Writing coordinate file...<br><br>Back Off! I just backed up prot_processed.gro to ./#prot_processed.gro.4#<br> --------- PLEASE NOTE ------------<br>You have succesfully generated a topology from: prot.pdb.<br>The oplsaa force field and the spce water model are used.<br>Note that the default
mechanism for selecting a force fields has<br>changed, starting from GROMACS version 3.2.0<br> --------- ETON ESAELP ------------ </body>
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