I tried SOL 44453 but I still the same error 01 Nisan 2011 15:11 tarihinde Mark Abraham <mark.abra...@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.abra...@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@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Ahmet YILDIRIM > > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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