[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 27 17:47:46 CEST 2008
Have you done anything else to your structure like adding solvent and ions? I'm
betting that's where this error is coming from. Check the .itp files produced
by pdb2gmx - the last line in the [ bonds ] section will give you a qtot (total
charge) for each molecule. If all of these values are not integers, then that's
the problem.
Otherwise, you have introduced a fragmented molecule (or many, given the
magnitude of the charge!) somewhere else in your preparation.
-Justin
Ragnarok sdf wrote:
> Hello Justin, sorry for the delay but I was trying repeat all my
> steps once more so that I was sure that the error would come out the
> same. It did.
>
> Here is a part of my itp file:
> ;
> ; File '1vkxdna_A.itp' was generated
> ; By user: onbekend (0)
> ; On host: onbekend
> ; At date: Wed Aug 27 11:46:27 2008
> ;
> ; This is your include topology file
> ; MY_DUPLEX
> ;
> [ moleculetype ]
> ; Name nrexcl
> Protein_A 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 amber99_25 1 DT5 H5T 1 0.4422 1.008 ;
> qtot 0.4422
> 2 amber99_43 1 DT5 O5' 2 -0.6318 16 ;
> qtot -0.1896
> 3 amber99_11 1 DT5 C5' 3 -0.0069 12.01 ;
> qtot -0.1965
> 4 amber99_19 1 DT5 H5'1 4 0.0754 1.008 ;
> qtot -0.1211
> 5 amber99_19 1 DT5 H5'2 5 0.0754 1.008 ;
> qtot -0.0457
> 6 amber99_11 1 DT5 C4' 6 0.1629 12.01 ;
> qtot 0.1172
> 7 amber99_19 1 DT5 H4' 7 0.1176 1.008 ;
> qtot 0.2348
> 8 amber99_44 1 DT5 O4' 8 -0.3691 16 ;
> qtot -0.1343
> 9 amber99_11 1 DT5 C1' 9 0.068 12.01 ;
> qtot -0.0663
> 10 amber99_20 1 DT5 H1' 10 0.1804 1.008 ;
> qtot 0.1141
> 11 amber99_40 1 DT5 N1 11 -0.0239 14.01 ;
> qtot 0.0902
> 12 amber99_7 1 DT5 C6 12 -0.2209 12.01 ;
> qtot -0.1307
> 13 amber99_23 1 DT5 H6 13 0.2607 1.008 ;
> qtot 0.13
> 14 amber99_7 1 DT5 C5 14 0.0025 12.01 ;
> qtot 0.1325
> 15 amber99_11 1 DT5 C7 15 -0.2269 12.01 ;
> qtot -0.0944
> 16 amber99_18 1 DT5 H71 16 0.077 1.008 ;
> qtot -0.0174
> 17 amber99_18 1 DT5 H72 17 0.077 1.008 ;
> qtot 0.0596
> 18 amber99_18 1 DT5 H73 18 0.077 1.008 ;
> qtot 0.1366
> 19 amber99_2 1 DT5 C4 19 0.5194 12.01 ;
> qtot 0.656
> 20 amber99_41 1 DT5 O4 20 -0.5563 16 ;
> qtot 0.0997
> 21 amber99_35 1 DT5 N3 21 -0.434 14.01 ;
> qtot -0.3343
> 22 amber99_25 1 DT5 H3 22 0.4422 1.008 ;
> qtot 0.1079
> 23 amber99_2 1 DT5 C2 23 0.5677 12.01 ;
> qtot 0.6756
> 24 amber99_41 1 DT5 O 24 -0.5881 16 ;
> qtot 0.0875
> 25 amber99_11 1 DT5 C3' 25 0.0713 12.01 ;
> qtot 0.1588
> 26 amber99_19 1 DT5 H3' 26 0.0985 1.008 ;
> qtot 0.2573
> 27 amber99_11 1 DT5 C2' 27 -0.0854 12.01 ;
> qtot 0.1719
> 28 amber99_18 1 DT5 H2'1 28 0.0718 1.008 ;
> qtot 0.2437
> 29 amber99_18 1 DT5 H2'2 29 0.0718 1.008 ;
> qtot 0.3155
> 30 amber99_44 1 DT5 O3' 30 -0.5232 16 ;
> qtot -0.2077
>
> Here is my pdb2gmx command line:
> pdb2gmx -f 1vkxdna.pdb -p 1vkxdna.top -o 1vkxdna.gro
>
> System charge still comes out as a non integer charge.
> System has non-zero total charge: -2.151740e+01
> Thank you again and sorry for the delay
>
>
>
>
> Ragnarok sdf wrote:
>
> > Tahnk you Justein for the reply.
> > I read again chapter 5, this time I tried to be more thorough,
> but still
> > I don't really understand why my topology is coming out bad. My .itp
> > files do not look like the one from the manual abou UREA. What i mean
> > is, the angles and bonds parts of the file have only 3 columns.
> Although
> > I read the manual, I am still not sure about the real problem here.
>
> There is no problem with only having three or four columns, per se.
> Amber
> topologies will be shown as such. The bonded parameters will be
> read from the
> ffamber*bon.itp file. Have you identified the atoms involved in the
> problematic
> bond(s) and angle(s)?
>
> > You mentioned that each residue should end up with an integer charge.
> > Well, mine don't.
> > What exactly do you mean with "post one of your nucleotides
> here"? From
> > my pdb file or from my itp generated files? The entire double
> helix with
> > all nucleotides or really just one of them?
>
> Post a single nucleotide from the topology. Sorry if I wasn't
> clear. What
> would be interesting to see is what charges and atom types you've
> been assigning
> to each nucleotide.
>
> > Sorry for asking these details. But I just want to make sure I don't
> > waste your time with useless posts.
>
> Much appreciated :)
>
> -Justin
>
> > Thank you again
> > And thank you in advance
> > Fabrício
> >
> >
> >
> ------------------------------------------------------------------------
> >
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 23 Aug 2008 23:29:33 +0300
> From: "Shay Amram" <shayamra at post.tau.ac.il
> <mailto:shayamra at post.tau.ac.il>>
> Subject: RE: [gmx-users] groups to write to trr
> To: <vvchaban at gmail.com <mailto:vvchaban at gmail.com>>,
> "'Discussion list for GROMACS users'"
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID: <20080823202940.593C5BEF6 at doar.tau.ac.il
> <mailto:20080823202940.593C5BEF6 at doar.tau.ac.il>>
> Content-Type: text/plain; charset="us-ascii"
>
> I think you should try using:
>
> trjconv -f file.trr -o file_with_groups_of_interest.trr -n index.ndx
>
>
>
> You should create the relevant index group (that includes all atoms of
> interest) before invoking the above command. You'll be prompted to
> choose a
> group so choose the group you created and trjconv will write an
> output trr
> that includes the group you picked alone.
>
>
>
> Hope that helps.
>
> -Shay
>
>
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>
> [mailto:gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>]
> On Behalf Of Vitaly Chaban
> Sent: Friday, August 22, 2008 14:05 PM
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Subject: [gmx-users] groups to write to trr
>
>
>
> Hi,
>
>
>
> Is it possible to write only the specified groups to the TRR
>
> trajectory like using xtc-grps key for XTC?
>
>
>
> We calculate VACFs and so need velocities to be written but only the
>
> velocity of some groups are of interest, not of all the particles. The
>
> "full" TRRs take extremely huge space...
>
>
>
>
>
> Thanks.
>
>
>
> --
>
> Vitaly V. Chaban
>
> School of Chemistry
>
> National University of Kharkiv
>
> Svoboda sq., 4, Kharkiv 61077, Ukraine
>
> email: chaban at univer.kharkov.ua <mailto:chaban at univer.kharkov.ua>
>
> skype: vvchaban
>
> _______________________________________________
>
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> End of gmx-users Digest, Vol 52, Issue 97
> *****************************************
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>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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