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Hi,<br><br>We are getting to much detail now.<br>In principle yes, but since you get a clear error message now, I wouldn't worry about this.<br>The chance that the last water block is willingly smaller than the 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 water<br>> <br>> Hi,<br>> <br>> Is it desirable that genion only considers a single SOL block? 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>> > From: iitdckc@gmail.com<br>> > Date: Thu, 11 Feb 2010 16:45:06 +0530<br>> > Subject: Re: [gmx-users] Software inconsistency error: Not 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 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, 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>> > 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>> > 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>> > 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 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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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