[gmx-users] The solvent group Water is not continuous
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 1 14:33:14 CEST 2011
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>> 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>>> 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>>> 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> | (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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