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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