[gmx-users] The solvent group Water is not continuous
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 1 14:44:21 CEST 2011
ahmet yıldırım wrote:
> When I created em.tpr I got the followings notes:
> *_NOTE 1 [file topol.top, line 52]:_*
> System has non-zero total charge: -1.500000e+01
>
> _*NOTE 2 [file topol.top]:*_
> The largest charge group contains 11 atoms.
> Since atoms only see each other when the centers of geometry of the charge
> groups they belong to are within the cut-off distance, too large charge
> groups can lead to serious cut-off artifacts.
> For efficiency and accuracy, charge group should consist of a few atoms.
> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>
> then, I tried to add ions.
>
Neither of these notes is relevant to the problem at hand, although the second
means that some component of your topology is badly broken.
Just to be very clear, after rearranging your .gro and .top such that (1) they
match and (2) all solvent molecules are continuous, you have created a new .tpr
file and you're still getting an error from genion?
-Justin
> Thanks
>
> 01 Nisan 2011 15:33 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> yazdı:
>
>
>
> ahmet yıldırım wrote:
>
> Dear users,
>
> I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.
>
>
> ...and hopefully did a complete re-parameterization of the nonsense
> charges it gives.
>
> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>
> That's an aside, completely unrelated to your actual problem, though.
>
>
> genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log
> select group:13
> Fatal error:
> The solvent group SOL is not continuous: index[984]=5334,
> index[985]=5355
> For more information and tips for troubleshooting, please check
> the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> You still haven't answered the second question I posed below. I
> assume this "em.tpr" file has not been re-generated from a properly
> continuous .gro and .top combination. If either were out of order
> with respect to the other (i.e. changing the .top and not the .gro),
> you would have gotten a fatal error from grompp when creating em.tpr.
>
> -Justin
>
>
>
> 01 Nisan 2011 15:17 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>> yazdı:
>
>
>
>
> ahmet yıldırım wrote:
>
> I tried SOL 44453 but I still the same error
>
>
> Are you using some index file that is specifying a discontinuous
> water group? Have you properly re-created your genion input .tpr
> file from this new topology?
>
> -Justin
>
> 01 Nisan 2011 15:11 tarihinde Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>>> yazdı:
>
>
> On 1/04/2011 11:03 PM, ahmet yıldırım wrote:
>
> Dear Dr. Mark,
>
> I did you said but I have the same error. please
> look at
> attached file
>
> topol.top:
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Protein_chain_B 1
> SOL 185
> SOL 143
> SOL 44125
> TRS 1
> EDO 1
>
>
> OK, well maybe it doesn't like different chunks of the
> same
> molecule
> even when they're adjacent in order. Try "SOL 44453"
> instead.
>
> Mark
>
>
> 01 Nisan 2011 14:41 tarihinde Mark Abraham
> <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>>> yazdı:
>
>
> On 1/04/2011 10:26 PM, ahmet yıldırım wrote:
>
> Dear Justin,
>
> I have Fatal Errror:The solvent group
> Water is not
> continuous. I look at gmx-users mailing list
> search. I
> also have the same problem.
> You
>
> said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
> It is exactly what I said; you've proven
> it. You have
> solvent, ligand, then
> solvent. To use genion (as the program
> prints out
> at the
> prompt) you must have
> a *continuous* group of solvent in order
> to embed
> ions. If
> you re-arrange the
>
> coordinate file and [molecules] section of the
> topology,
> you can achieve this.
>
> How can I do the re-arrange you said? Can you
> explain a
> little bit?
>
>
> You need a system topology whose molecules are
> ordered such
> that all the water is contiguous. That means the
> order of the
> names of molecule types in your [ molecules ]
> section
> of your
> .top can have only one mention of water. Since the
> order of
> molecules in the coordinate file must match this
> order, you
> will need to physically reorder your [ molecules ]
> section,
> and the chunks of molecules in your coordinate
> file.
> Fortunately, you don't have to renumber those
> atoms
> in the
> coordinate file.
>
> Mark
>
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> -- Ahmet YILDIRIM
>
>
>
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> -- Ahmet YILDIRIM
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> Ahmet YILDIRIM
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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
>
> ========================================
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> --
> Ahmet YILDIRIM
--
========================================
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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