Hello gmxusers !!<br>I am simulating a protein and it is bound to ATP.<br>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.<br>
Error:<br><br><br clear="all">$ 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 /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>Group 0 ( System) has 70056 elements <br>
Group 1 ( Protein) has 10214 elements <br>Group 2 ( Protein-H) has 5107 elements <br>Group 3 ( C-alpha) has 623 elements <br>
Group 4 ( Backbone) has 1869 elements <br>Group 5 ( MainChain) has 2488 elements <br>Group 6 (MainChain+Cb) has 3083 elements <br>
Group 7 ( MainChain+H) has 3099 elements <br>Group 8 ( SideChain) has 7115 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. 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>