[gmx-users] The solvent group Water is not continuous
ahmet yıldırım
ahmedo047 at gmail.com
Fri Apr 1 14:40:55 CEST 2011
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.
Thanks
01 Nisan 2011 15:33 tarihinde Justin A. Lemkul <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>> 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
>>
>> -- gmx-users mailing list
>> gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org
>> <mailto: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
>> <mailto:gmx-users-request at gromacs.org>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>.
>>
>> Can't post? Read
>> http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> -- Ahmet YILDIRIM
>>
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto: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
>> <mailto:gmx-users-request at gromacs.org>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>.
>>
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> -- 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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto: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
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> --
> 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
>
--
Ahmet YILDIRIM
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110401/1548b5bc/attachment.html>
More information about the gromacs.org_gmx-users
mailing list