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 <jalem...@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 <jalem...@vt.edu <mailto: >> jalem...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au> >> <mailto:mark.abra...@anu.edu.au >> <mailto: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 <mailto:mark.abra...@anu.edu.au> >> <mailto:mark.abra...@anu.edu.au >> <mailto: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 <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto: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 >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@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@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@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@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
