[gmx-users] # Protein non-integer charge‏

Mon Mar 7 15:11:45 CET 2011

Hi everybody,

My problem is the following: I am studying the chromosome partitioning protein ParB from Burkholderia cenocepacia J2315. As no crystal structure was available, I used I-TASSER to predict its 3d structure.

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.

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.

PDB file: http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S64445/

Best regards,

Marcelo

------------------------------------------------------------------------

pdb2gmx output:

Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading prot.pdb...
Read 'protein', 4573 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 297 residues with 4573 atoms

  chain  #res #atoms
  1 'A'   297   4573  

All occupancies are one
Opening library file /usr/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
Residue 59
Sorting it all out...
Opening library file /usr/share/gromacs/top/ffoplsaa.hdb
Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb
Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb

Back Off! I just backed up topol.top to ./#topol.top.7#
Processing chain 1 'A' (4573 atoms, 297 residues)
There are 451 donors and 430 acceptors
There are 670 hydrogen bonds
Will use HISB for residue 137
Will use HISB for residue 150
Will use HISB for residue 190
Will use HISB for residue 207
Will use HISB for residue 225
Checking for duplicate atoms....
Opening library file /usr/share/gromacs/top/specbond.dat
7 out of 7 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
                    MET1   MET53   MET71  MET119 HISB137 HISB150  MET180
                    SD10   SD795  SD1051  SD1801 NE22091 NE22301  SD2752
   MET53   SD795   2.734
   MET71  SD1051   3.599   1.900
  MET119  SD1801   3.866   2.738   1.752
 HISB137 NE22091   3.420   2.337   2.726   1.784
 HISB150 NE22301   3.300   3.399   3.547   2.251   1.488
  MET180  SD2752   2.714   2.430   3.872   3.588   2.019   2.534
  MET188  SD2867   1.831   2.554   3.389   2.903   1.893   1.645   1.520
 HISB190 NE22894   1.854   2.621   3.979   3.803   2.535   2.621   1.015
 HISB207 NE23144   3.293   3.005   4.536   4.229   2.555   3.052   0.734
  MET214  SD3267   2.343   3.284   4.746   4.546   3.162   3.163   1.349
 HISB225 NE23449   3.197   4.310   5.713   5.308   3.829   3.582   2.113
                  MET188 HISB190 HISB207  MET214
                  SD2867 NE22894 NE23144  SD3267
 HISB190 NE22894   1.112
 HISB207 NE23144   2.169   1.485
  MET214  SD3267   1.790   0.783   1.422
 HISB225 NE23449   2.522   1.762   1.900   1.063
N-terminus: NH3+
C-terminus: COO-
Now there are 297 residues with 4577 atoms
Making bonds...
Opening library file /usr/share/gromacs/top/aminoacids.dat
Number of bonds was 4596, now 4596
Generating angles, dihedrals and pairs...
Before cleaning: 12035 pairs
Before cleaning: 12105 dihedrals
Keeping all generated dihedrals
There are 12105 dihedrals,  838 impropers, 8351 angles
          12017 pairs,     4596 bonds and     0 virtual sites
Total mass 32038.885 a.m.u.
Total charge -4.680 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.4#

Writing coordinate file...

Back Off! I just backed up prot_processed.gro to ./#prot_processed.gro.4#
        --------- PLEASE NOTE ------------
You have succesfully generated a topology from: prot.pdb.
The oplsaa force field and the spce water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
        --------- ETON ESAELP ------------ 		 	   		  
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