[gmx-users] Newbie: How to modify the topology file after adding ions?
Jose Borreguero
borreguero at gmail.com
Fri Dec 9 01:54:58 CET 2011
Dear Tsjerk,
I never thought I was being rude, probably because I was upset at the time.
I apologize.
Unfortunately, I believe you'll get more of the same in the future if you
don't spend more time updating your page. Devilish details like Na or Na+
have no place in a tutorial. There will be ample time later for these, when
one has to fence with his own projects.
Thanks for updating the tutorial.
Best regards,
Jose
On Thu, Dec 8, 2011 at 4:11 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Jose,
>
> The references to NA+ and CL- have been changed, you can reload the
> page in your browser if you care to continue. Now I still think your
> statement was rather rude and showing disrespect to the time I put in
> the tutorial. Apart from the reference to NA/CL you're also factually
> incorrect in your statements. The first sentence of the second
> paragraph under the heading 'Hands on ...' (top of the page) reads:
>
> """
> This tutorial uses Gromacs (http://www.gromacs.org) version 4.5 and
> most of the commands given are specific to this package.
> """
>
> Later on that page, considering the addition of ions to the topology
> there is the statement:
>
> """
> Note the numbers of ions added, and verify that an excess of sodium
> ions is added for neutralization. Having replaced a number of water
> molecules with ions, the system topology in protein.top is not correct
> anymore. Edit the topology file and decrease the number of solvent
> molecules. Also add a line specifying the number of NA ions and a line
> specifying the amount of CL.
> """
>
> You may note I changed NA+ to NA and CL- to CL, but for the rest the
> paragraph was not edited or added.
>
> Although I feel personally addressed, I can add that you're not the
> first to respond to the tutorial like this. It is common behaviour for
> a subset of undergrad students that had to follow this course as part
> of their curriculum. And the default answer is usually one of "read",
> "read again" or "read better!".
>
> Cheers,
>
> Tsjerk
>
>
> On Wed, Dec 7, 2011 at 8:29 PM, Jose Borreguero <borreguero at gmail.com>
> wrote:
> > This tutorial doesn't seem to be quite useful, if so many errors pop up.
> > Maybe it was implemented for Gromacs < 4.5.x but there's no info on the
> > version it should be used.
> >
> > However, Lo and behold! I found that you have a nice page with Gromacs
> 4.5.x
> > tutorials :D
> > (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
> )
> > I'll give a try with the Lyzosyme one!
> >
> > - Jose
> >
> >
> > On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <jalemkul at vt.edu>
> wrote:
> >>
> >>
> >>
> >> Jose Borreguero wrote:
> >>>
> >>> Hi Justin, thanks for your reply!
> >>>
> >>> I appended '-p protein.top' to genion. File protein.top was
> automatically
> >>> updated by insertion of the following lines at the end of the file:
> >>> /[ molecules ]
> >>>
> >>> ; Compound #mols
> >>> Protein_chain_A 1
> >>> SOL 7791
> >>> NA+ 26
> >>> CL- 23/
> >>>
> >>>
> >>> My solvated PDB, protein-solvent.pdb contains lines like these:
> >>> ATOM 24543 NA NA+ 8043 50.712 66.452 12.341 1.00 0.00
> >>>
> >>> Now when I run grommp, I get the error
> >>> /Fatal error:
> >>> No such moleculetype NA+/
> >>>
> >>>
> >>> I checked file gromos45a3.ff/ions.itp. The sodium is included in this
> >>> fashion:
> >>> /[ moleculetype ]
> >>>
> >>> ; molname nrexcl
> >>> NA 1
> >>> [ atoms ]
> >>> ; id at type res nr residu name at name cg nr charge mass
> >>> 1 NA+ 1 NA NA 1 22.9898/
> >>>
> >>>
> >>> It seems the naming convention of ions.itp is different than that of
> >>> protein.top and protein-solvent.pdb. I changed protein.top and
> >>
> >>
> >> What was your exact genion command? If you tell genion to use "-pname
> >> NA+" (which is wrong) you get this result. Note that the error says the
> >> moleculetype "NA+" is not found; the moleculetype name is "NA" instead.
> >>
> >>> protein-solvent.pdb to match the naming of ions.itp. Then when I run
> >>> grompp I get the error:
> >>> /ERROR 1 [file protein.top, line 7228]:
> >>>
> >>> ERROR: One of the box lengths is smaller than twice the cut-off
> length.
> >>> Increase the box size or decrease rlist./
> >>>
> >>> The puzzling thing is that line 7228 of protein.top is the last line of
> >>> the file, that is,
> >>> CL 23
> >>> So the error message is not much help :(
> >>
> >>
> >> The problem comes from the coordinate file and settings of the .mdp
> file;
> >> they are somehow incompatible such that they would cause a violation of
> the
> >> minimum image convention. Why the error points to the .top I cannot
> say.
> >>
> >>
> >> -Justin
> >>
> >> --
> >> ========================================
> >>
> >> 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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> >
> >
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list gmx-users at gromacs.org
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