[gmx-users] # Protein non-integer charge‏

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 7 15:44:53 CET 2011



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: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > 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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