[gmx-users] # Protein non-integer charge‏

Mon Mar 7 15:17:28 CET 2011

On 8/03/2011 1:11 AM, Marcelo Silva wrote:
> 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.

Usually that means it thinks it's done what you've asked. It is possible 
to choose inappropriate duplicate termini, and such, and this does not 
flag an error. You should look at the [atoms] section of your .top. Each 
residue should have an integral charge (i.e. the qtot column is an 
integer). See where this goes wrong.

Mark

> 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< br>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 N E22091 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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