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Hi,<br><br>Yes, but there are (currently) two independent steps in genion.<br>First water is replaced using the index group that the users selected<br>and then the top file is edited. They two steps are independent.<br>There are no checks that the index group actually matches the topology<br>molecule sections (and strictly speaking they don't have to either).<br>But it would be better to link the two steps, although I don't think I want<br>to spend more time on this.<br><br>Berk<br><br>> Date: Thu, 11 Feb 2010 13:29:06 +0000<br>> From: t.piggot@bristol.ac.uk<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Software inconsistency error: Not enough water<br>> <br>> Sure, that's why I think it is a good idea to do what you said and just <br>> have genion use the final SOL block (normally added through genbox, so <br>> not containing the crystal waters) rather than use all of the SOL blocks.<br>> <br>> Tom<br>> <br>> Berk Hess wrote:<br>> > Hi,<br>> > <br>> > Yes, but genion is not smart enough (yet) to see the difference between <br>> > crystal water and normal water.<br>> > <br>> > Berk<br>> > <br>> > > Date: Thu, 11 Feb 2010 13:07:41 +0000<br>> > > From: t.piggot@bristol.ac.uk<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Software inconsistency error: Not enough water<br>> > ><br>> > > Plus I suppose that if you have kept the crystal waters you would not<br>> > > want them to be replaced by genion.<br>> > ><br>> > > Tom<br>> > ><br>> > > Berk Hess wrote:<br>> > > > Hi,<br>> > > ><br>> > > > We are getting to much detail now.<br>> > > > In principle yes, but since you get a clear error message now, I<br>> > > > wouldn't worry about this.<br>> > > > The chance that the last water block is willingly smaller than the<br>> > > > number of ions is about zero.<br>> > > ><br>> > > > Berk<br>> > > ><br>> > > > > Date: Thu, 11 Feb 2010 13:34:59 +0100<br>> > > > > From: erikm@xray.bmc.uu.se<br>> > > > > To: gmx-users@gromacs.org<br>> > > > > Subject: Re: [gmx-users] Software inconsistency error: Not enough <br>> > water<br>> > > > ><br>> > > > > Hi,<br>> > > > ><br>> > > > > Is it desirable that genion only considers a single SOL block? <br>> > Why not<br>> > > > > use them all if there are many?<br>> > > > ><br>> > > > > Regards,<br>> > > > ><br>> > > > > Erik<br>> > > > ><br>> > > > > Berk Hess skrev:<br>> > > > > > Hi,<br>> > > > > ><br>> > > > > > genion in future Gromacs versions will only use the last SOL block<br>> > > > > > and give a proper error message when there is not enough water.<br>> > > > > ><br>> > > > > > Berk<br>> > > > > ><br>> > > > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > > > From: iitdckc@gmail.com<br>> > > > > > Date: Thu, 11 Feb 2010 16:45:06 +0530<br>> > > > > > Subject: Re: [gmx-users] Software inconsistency error: Not <br>> > enough water<br>> > > > > > To: gmx-users@gromacs.org<br>> > > > > ><br>> > > > > ><br>> > > > > > Thanks berk.<br>> > > > > > By the way, if I dont give -p topol.top as input to genion, then<br>> > > > > > genion executes. In this case, I manually edit the topology <br>> > file and<br>> > > > > > add the ion information.<br>> > > > > > [ molecules ]<br>> > > > > > ; Compound #mols<br>> > > > > > Protein_A 1<br>> > > > > > Protein_B 1<br>> > > > > > Protein_C 1<br>> > > > > > Protein_D 1<br>> > > > > > Protein_E 1<br>> > > > > > SOL 32<br>> > > > > > SOL 46<br>> > > > > > SOL 3<br>> > > > > > SOL 13<br>> > > > > > SOL 19791<br>> > > > > > Na 48<br>> > > > > ><br>> > > > > > This is my part of topology after adding ions (Na). In the previous<br>> > > > > > case of genion was only considering first SOL information, <br>> > which has<br>> > > > > > only 32 molecules.<br>> > > > > ><br>> > > > > > Chandan<br>> > > > > ><br>> > > > > ><br>> > > > > > --<br>> > > > > > Chandan kumar Choudhury<br>> > > > > > NCL, Pune<br>> > > > > > INDIA<br>> > > > > ><br>> > > > > ><br>> > > > > > On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess <gmx3@hotmail.com<br>> > > > > > <mailto:gmx3@hotmail.com>> wrote:<br>> > > > > ><br>> > > > > > Hi,<br>> > > > > ><br>> > > > > > This error message in incorrect, it is probably not a software<br>> > > > > > inconsistency.<br>> > > > > > Looking at the code, it seems the problem is that the topology file<br>> > > > > > you provided does not have enough SOL molecules in the [molecules<br>> > > > > > ] section.<br>> > > > > > I'll fix this error message for the next release.<br>> > > > > ><br>> > > > > > Berk<br>> > > > > ><br>> > > > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > > > From: iitdckc@gmail.com <mailto:iitdckc@gmail.com><br>> > > > > > Date: Thu, 11 Feb 2010 12:48:53 +0530<br>> > > > > > To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org><br>> > > > > > Subject: [gmx-users] Software inconsistency error: Not enough water<br>> > > > > ><br>> > > > > ><br>> > > > > > Hello gmxusers !!<br>> > > > > > I am simulating a protein and it is bound to ATP.<br>> > > > > > Simulation of protein alone (without) works fine. Solely ATP<br>> > > > > > simulation too works. But the problem arises on adding ions to the<br>> > > > > > protein + ATP (1QHH.pdb) file.<br>> > > > > > Error:<br>> > > > > ><br>> > > > > ><br>> > > > > > $ genion -s em.tpr -o ion.pdb -p topol.top -np 48<br>> > > > > > WARNING: turning of free energy, will use lambda=0<br>> > > > > > Reading file em.tpr, VERSION 4.0.7 (single precision)<br>> > > > > > Using a coulomb cut-off of 0.9 nm<br>> > > > > > Will try to add 48 Na ions and 0 Cl ions.<br>> > > > > > Select a continuous group of solvent molecules<br>> > > > > > Opening library file<br>> > > > > > /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>> > > > > > Group 0 ( System) has 70056<br>> > > > > > elements<br>> > > > > > Group 1 ( Protein) has 10214<br>> > > > > > elements<br>> > > > > > Group 2 ( Protein-H) has 5107<br>> > > > > > elements<br>> > > > > > Group 3 ( C-alpha) has 623<br>> > > > > > elements<br>> > > > > > Group 4 ( Backbone) has 1869<br>> > > > > > elements<br>> > > > > > Group 5 ( MainChain) has 2488<br>> > > > > > elements<br>> > > > > > Group 6 (MainChain+Cb) has 3083<br>> > > > > > elements<br>> > > > > > Group 7 ( MainChain+H) has 3099<br>> > > > > > elements<br>> > > > > > Group 8 ( SideChain) has 7115<br>> > > > > > elements<br>> > > > > > Group 9 ( SideChain-H) has 2619 elements<br>> > > > > > Group 10 ( Prot-Masses) has 10214 elements<br>> > > > > > Group 11 ( Non-Protein) has 59842 elements<br>> > > > > > Group 12 ( ATP) has 43 elements<br>> > > > > > Group 13 ( SOL) has 59799 elements<br>> > > > > > Group 14 ( Other) has 59842 elements<br>> > > > > > Select a group: 13<br>> > > > > > Selected 13: 'SOL'<br>> > > > > > Number of (3-atomic) solvent molecules: 19933<br>> > > > > ><br>> > > > > > Processing topology<br>> > > > > ><br>> > > > > > Back Off! I just backed up temp.top to ./#temp.top.1#<br>> > > > > ><br>> > > > > > -------------------------------------------------------<br>> > > > > > Program genion, VERSION 4.0.7<br>> > > > > > Source code file: gmx_genion.c, line: 269<br>> > > > > ><br>> > > > > > Software inconsistency error:<br>> > > > > > Not enough water<br>> > > > > > -------------------------------------------------------<br>> > > > > ><br>> > > > > > Though my system has sufficient amount of water (19933) molecules.<br>> > > > > > Can not understand the error. Any information would be useful.<br>> > > > > ><br>> > > > > ><br>> > > > > > Chadan<br>> > > > > > --<br>> > > > > > Chandan kumar Choudhury<br>> > > > > > NCL, Pune<br>> > > > > > INDIA<br>> > > > > ><br>> > > > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > > > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > > > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > > > ><br>> > > > > > --<br>> > > > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > > > <mailto:gmx-users@gromacs.org><br>> > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > > > > Please search the archive at http://www.gromacs.org/search before<br>> > > > > > posting!<br>> > > > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > > > www interface or send it to gmx-users-request@gromacs.org<br>> > > > > > <mailto:gmx-users-request@gromacs.org>.<br>> > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > > > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > > > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > > ><br>> > > > ><br>> > > > > --<br>> > > > > -----------------------------------------------<br>> > > > > Erik Marklund, PhD student<br>> > > > > Laboratory of Molecular Biophysics,<br>> > > > > Dept. of Cell and Molecular Biology, Uppsala University.<br>> > > > > Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> > > > > phone: +46 18 471 4537 fax: +46 18 511 755<br>> > > > > erikm@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys<br>> > > > ><br>> > > > > --<br>> > > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > > > Please search the archive at http://www.gromacs.org/search before<br>> > > > posting!<br>> > > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > ><br>> > ><br>> > > --<br>> > > Thomas Piggot<br>> > > University of Bristol, UK.<br>> > > --<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > ------------------------------------------------------------------------<br>> > New Windows 7: Find the right PC for you. Learn more. <br>> > <http://windows.microsoft.com/shop><br>> > <br>> <br>> -- <br>> Thomas Piggot<br>> University of Bristol, UK.<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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