*Hi everyone. I have a problem when I try to run GENION, GROMACS says: * WARNING: turning of free energy, will use lambda=0 Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 0 Na ions and 15 NA+ ions. Select a continuous group of solvent molecules Opening library file /usr/share/gromacs/top/ aminoacids.dat Group 0 ( System) has 275439 elements Group 1 ( Protein) has 1722 elements Group 2 ( Protein-H) has 1371 elements Group 3 ( C-alpha) has 185 elements Group 4 ( Backbone) has 555 elements Group 5 ( MainChain) has 741 elements Group 6 (MainChain+Cb) has 909 elements Group 7 ( MainChain+H) has 921 elements Group 8 ( SideChain) has 801 elements Group 9 ( SideChain-H) has 630 elements Group 10 ( Prot-Masses) has 1722 elements Group 11 ( Non-Protein) has 273717 elements Group 12 ( ZN) has 1 elements Group 13 ( SOL) has 273702 elements Group 14 ( LIG) has 14 elements Group 15 ( Other) has 273717 elements Select a group: 13 Selected 13: 'SOL'
------------------------------------------------------- Program genion, VERSION 3.3.3 Source code file: ../../../../src/tools/gmx_genion.c, line: 429 Fatal error: The solvent group SOL is not continuous: index[9]=1732, index[10]=1747 ------------------------------------------------------- "Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is." (Jackie Brown) *I do not know the reason,the number of residues in top file and pdb file are the same. The only warning that I saw was when I ran grompp: * WARNING 1 [file 1x8a.top, line unknown]: 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. *Coincidentally they are some of the atomos of my ligand* * I have been reading the web and no-one says nothing about it. I would be very grateful if someone can help me or give me advices. Best Regards MIguel Quiliano*
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