Dear users, I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.
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 01 Nisan 2011 15:17 tarihinde Justin A. Lemkul <[email protected]> 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 <[email protected]<mailto: >> [email protected]>> 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 >>> <[email protected] <mailto:[email protected]>> 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 [email protected] >>> <mailto:[email protected]> >>> >>> 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 [email protected] >>> <mailto:[email protected]>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >>> -- Ahmet YILDIRIM >>> >> >> >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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