[gmx-users] # Protein non-integer charge
Marcelo Silva
jokler79 at hotmail.com
Mon Mar 7 16:27:52 CET 2011
Thank you Justin, that was exactly the problem. When I ran pdb2gmx in
another computer it worked fine. I must have changed the .rtp file.
Best regards,
Marcelo
Em 07-03-2011 15:14, Justin A. Lemkul escreveu:
>
>
> 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
>> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > > > Please don't post (un)subscribe requests to the list. Use the
>> > > > www interface or send it to gmx-users-request at gromacs.org.
>> > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > --
>> > ========================================
>> >! !
>> > 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!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
More information about the gromacs.org_gmx-users
mailing list