[gmx-users] # Protein non-integer charge‏

[Justin A. Lemkul]

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.
> 

This usually happens when you've chosen termini incorrectly.  The tutorial 
doesn't require you to select termini, since the defaults (NH3+ and COO-) are 
correct.  Are you choosing something else?  Usually with OPLS the problem is 
choosing zwitterionic termini when not dealing with a single amino acid, which 
is the only time these termini are appropriate.

-Justin

> 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 ------------
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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