Marcelo Silva wrote:
Thank you Mark and Justin,
I didn't specified the termini, but when I choose the zwitterionic forms
the net charge becomes -4.670.
You shouldn't; as I said before, zwitterionic termini are only for single amino
acids, not full-length proteins.
Without specifying the termini, the first non integer residue is residue
nr. 12 arginine: qtot 4 to qtot 4.82.
Are you missing any atoms? What was your exact pdb2gmx command?
-Justin
If both termini are in the zwitterionic forms, the error is right at the
1st residue (methionine): total charge: 0.9
> Date: Mon, 7 Mar 2011 09:21:08 -0500
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] # Protein non-integer charge
>
>
>
> 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
f! ! ile
> > 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/
> >
> > Be! ! st 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
&! ! gt; > /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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--
========================================
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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