Thanks berk. By the way, if I dont give -p topol.top as input to genion, then genion executes. In this case, I manually edit the topology file and add the ion information. [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 Protein_C 1 Protein_D 1 Protein_E 1 SOL 32 SOL 46 SOL 3 SOL 13 SOL 19791 Na 48
This is my part of topology after adding ions (Na). In the previous case of genion was only considering first SOL information, which has only 32 molecules. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess <g...@hotmail.com> wrote: > Hi, > > This error message in incorrect, it is probably not a software > inconsistency. > Looking at the code, it seems the problem is that the topology file > you provided does not have enough SOL molecules in the [molecules ] > section. > I'll fix this error message for the next release. > > Berk > > ------------------------------ > From: iitd...@gmail.com > Date: Thu, 11 Feb 2010 12:48:53 +0530 > To: gmx-users@gromacs.org > Subject: [gmx-users] Software inconsistency error: Not enough water > > > Hello gmxusers !! > I am simulating a protein and it is bound to ATP. > Simulation of protein alone (without) works fine. Solely ATP simulation too > works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb) > file. > Error: > > > $ genion -s em.tpr -o ion.pdb -p topol.top -np 48 > WARNING: turning of free energy, will use lambda=0 > Reading file em.tpr, VERSION 4.0.7 (single precision) > Using a coulomb cut-off of 0.9 nm > Will try to add 48 Na ions and 0 Cl ions. > Select a continuous group of solvent molecules > Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat > Group 0 ( System) has 70056 elements > Group 1 ( Protein) has 10214 elements > Group 2 ( Protein-H) has 5107 elements > Group 3 ( C-alpha) has 623 elements > Group 4 ( Backbone) has 1869 elements > Group 5 ( MainChain) has 2488 elements > Group 6 (MainChain+Cb) has 3083 elements > Group 7 ( MainChain+H) has 3099 elements > Group 8 ( SideChain) has 7115 elements > Group 9 ( SideChain-H) has 2619 elements > Group 10 ( Prot-Masses) has 10214 elements > Group 11 ( Non-Protein) has 59842 elements > Group 12 ( ATP) has 43 elements > Group 13 ( SOL) has 59799 elements > Group 14 ( Other) has 59842 elements > Select a group: 13 > Selected 13: 'SOL' > Number of (3-atomic) solvent molecules: 19933 > > Processing topology > > Back Off! I just backed up temp.top to ./#temp.top.1# > > ------------------------------------------------------- > Program genion, VERSION 4.0.7 > Source code file: gmx_genion.c, line: 269 > > Software inconsistency error: > Not enough water > ------------------------------------------------------- > > Though my system has sufficient amount of water (19933) molecules. Can not > understand the error. Any information would be useful. > > > Chadan > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > -- > 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/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/mailing_lists/users.php >
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