Hi<div><br></div><div>I am using editconf to set my box to the right size using:</div><div><br></div><div>editconf -f in.gro -o out.gro -box 30 30 30</div><div><br></div><div>gromacs v. 4.5.3</div><div><br></div><div>For this example, my system contains a phosphate anion and a water molecule. After editconf runs, it changes the residue name SOL of the water molecule to the residue name PHO for phosphate, because both have the same residue number (1). Is this not a bug, or am I doing something really silly? One can always try to run a simulation of an amino acid in water, and the error below would be replicated? </div>
<div><br></div><div>Interestingly, grompp does not complain that the residue PHO has 8 atoms instead of 5 as in the topology file.</div><div><br></div><div>I do not see this problem if the residue number of the water molecule is 2 instead of 1.</div>
<div><br></div><div>Below are the two .gro files, before and after running the above command.</div><div><br></div><div><br></div><div><div>GROtesk MACabre and Sinister</div><div>8</div><div> 1PHO O1P 1 13.422 2.753 5.900</div>
<div> 1PHO P 2 13.250 2.818 5.976</div><div> 1PHO O2P 3 13.193 2.967 5.853</div><div> 1PHO O3P 4 13.263 2.864 6.169</div><div> 1PHO O4P 5 13.118 2.672 5.939</div><div>
1SOL OW 1 12.025 1.421 -1.203</div><div> 1SOL HW1 2 12.125 1.421 -1.203</div><div> 1SOL HW2 3 11.993 1.516 -1.203</div><div>20 20 20</div><div><br></div><div><br></div><div>GROtesk MACabre and Sinister</div>
<div> 8</div><div> 1PHO O1P 1 15.623 15.449 17.622</div><div> 1PHO P 2 15.451 15.514 17.697</div><div> 1PHO O2P 3 15.394 15.663 17.574</div><div> 1PHO O3P 4 15.464 15.560 17.890</div>
<div> 1PHO O4P 5 15.319 15.368 17.660</div><div> 1PHO OW 6 14.226 14.117 10.518</div><div> 1PHO HW1 7 14.326 14.117 10.518</div><div> 1PHO HW2 8 14.194 14.212 10.518</div><div>
30.00000 30.00000 30.00000</div><div><br></div><div><br></div><div><br></div><div><br></div><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>
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