[gmx-users] # Protein non-integer charge‏

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 7 16:14:48 CET 2011



Marcelo Silva wrote:
> The pdb command was: pdb2gmx -f prot.pdb -o prot_processed.gro -water spce
> 
> There is a total of 297 residues. The pdb2gmx indicates that there are 
> 4573 atoms but the topology file indicates 4577 atoms.
> 
> It seems that is the arginine residue that is having problems:
> 
>    172   opls_236     11    GLY      O     56       -0.5    15.9994   ; 
> qtot 4
>    173   opls_238     12    ARG      N     57       -0.5    14.0067   ; 
> qtot 3.5
>    174   opls_241     12    ARG      H     57        0.3      1.008&nb! 
> ! sp;  ; qtot 3.8
>    175  opls_224B     12    ARG     CA     57       0.14     12.011   ; 
> qtot 3.94
>    176   opls_140     12    ARG     HA     57       0.06      1.008   ; 
> qtot 4
>    177   opls_136     12    ARG     CB     58      -0.12     12.011   ; 
> qtot 3.88
>    178   opls_140     12    ARG    HB1     58       0.06      1.008   ; 
> qtot 3.94
>    17! ! 9   opls_140     12    ARG    HB2     58       0.06      
> 1.008   ; qtot 4
>    180   opls_308     12    ARG     CG     59      -0.05     12.011   ; 
> qtot 3.95
>    181   opls_140     12    ARG    HG1     59       0.06      1.008   ; 
> qtot 4.01
>    182   opls_140     12    ARG    HG2     59      -0.12      1.008   ; 
> qtot 3.89

More specifically, atom HG2 is having problems.  It should be assigned a charge 
of +0.06, not -0.12.  The .rtp file distributed with Gromacs 4.5.3 is correct, 
so I don't know how this is happening unless someone has messed with your .rtp 
file.  This difference of -0.18 accounts for the spurious charge.

-Justin

>    183   opls_307   &nbs! ! p; 12    ARG     CD     60       0.19     
> 12.011   ; qtot 4.08
>    184   opls_140     12    ARG    HD1     60       0.06      1.008   ; 
> qtot 4.14
>    185   opls_140     12    ARG    HD2     60       0.06      1.008   ; 
> qtot 4.2
>    186   opls_303     12    ARG     NE     61       -0.7    14.0067   ; 
> qtot 3.5
>    187   opls_304     12    ARG  ! ! ;   HE     61       0.44      
> 1.008   ; qtot 3.94
>    188   opls_302     12    ARG     CZ     61       0.64     12.011   ; 
> qtot 4.58
>    189   opls_300     12    ARG    NH1     62       -0.8    14.0067   ; 
> qtot 3.78
>    190   opls_301     12    ARG   HH11     62       0.46      1.008   ; 
> qtot 4.24
>    191   opls_301     12    ARG   HH12     62 &n! ! bsp;     0.46      
> 1.008   ; qtot 4.7
>    192   opls_300     12    ARG    NH2     63       -0.8    14.0067   ; 
> qtot 3.9
>    193   opls_301     12    ARG   HH21     63       0.46      1.008   ; 
> qtot 4.36
>    194   opls_301     12    ARG   HH22     63       0.46      1.008   ; 
> qtot 4.82
>    195   opls_235     12    ARG      C     64        0.5 ! ! ;    
> 12.011   ; qtot 5.32
>    196   opls_236     12    ARG      O     64       -0.5    15.9994   ; 
> qtot 4.82
> 
> ----------------------
> 
>    725   opls_236     49    PRO      O    237       -0.5    15.9994   ; 
> qtot 3.82
>    726   opls_238     50    ARG      N    238       -0.5    14.0067   ; 
> qtot 3.32
>    727   opls_241     50    ARG      H    238        0.3 &! ! nbsp;    
> 1.008   ; qtot 3.62
>    728  opls_224B     50    ARG     CA    238       0.14     12.011   ; 
> qtot 3.76
>    729   opls_140     50    ARG     HA    238       0.06      1.008   ; 
> qtot 3.82
>    730   opls_136     50    ARG     CB    239      -0.12     12.011   ; 
> qtot 3.7
>    731   opls_140     50    ARG    HB1    239       0.06      1.008   ; 
> qtot 3.76
> ! !    732   opls_140     50    ARG    HB2    239       0.06      
> 1.008   ; qtot 3.82
>    733   opls_308     50    ARG     CG    240      -0.05     12.011   ; 
> qtot 3.77
>    734   opls_140     50    ARG    HG1    240       0.06      1.008   ; 
> qtot 3.83
>    735   opls_140     50    ARG    HG2    240      -0.12      1.008   ; 
> qtot 3.71
>    736   opls_307    ! ! 50    ARG     CD    241       0.19     12.011   
> ; qtot 3.9
>    737   opls_140     50    ARG    HD1    241       0.06      1.008   ; 
> qtot 3.96
>    738   opls_140     50    ARG    HD2    241       0.06      1.008   ; 
> qtot 4.02
>    739   opls_303     50    ARG     NE    242       -0.7    14.0067   ; 
> qtot 3.32
>    740   opls_304     50    ARG     HE ! ! ;   242       0.44      
> 1.008   ; qtot 3.76
>    741   opls_302     50    ARG     CZ    242       0.64     12.011   ; 
> qtot 4.4
>    742   opls_300     50    ARG    NH1    243       -0.8    14.0067   ; 
> qtot 3.6
>    743   opls_301     50    ARG   HH11    243       0.46      1.008   ; 
> qtot 4.06
>    744   opls_301     50    ARG   HH12    243       0.46  &nb! ! sp;   
> 1.008   ; qtot 4.52
>    745   opls_300     50    ARG    NH2    244       -0.8    14.0067   ; 
> qtot 3.72
>    746   opls_301     50    ARG   HH21    244       0.46      1.008   ; 
> qtot 4.18
>    747   opls_301     50    ARG   HH22    244       0.46      1.008   ; 
> qtot 4.64
>    748   opls_235     50    ARG      C    245        0.5     12.011   ; 
> qtot 5.14
>   ! ! 749   opls_236     50    ARG      O    245       -0.5    15.9994   
> ; qtot 4.64
> 
>  > Date: Mon, 7 Mar 2011 09:44:53 -0500
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] # Protein non-integer charge‏
>  >
>  >
>  >
>  > 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, whi! ! ch
>  > > > 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 li! ! brary 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 SD7! ! 95 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
>  > > > I! ! CTAS 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
>  > > >
>  > > >! ! ========================================
>  > > > --
>  > > > gmx-users mailing list gmx-users at gromacs.org
>  > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > > > Please search the archive at
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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
>  >
>  > ========================================
>  > --
>  > gmx-users mailing list gmx-users at gromacs.org
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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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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