Hi all,<br><br>I recently started molecular dynamics with gromacs performing protein-ligand simulations for my project first i worked out example from justin tutorials on protein ligand system and trying to apply to my protein and ligand.<br>
<br>First i generated topology for my protein using pdbgmx and then i used PRODRG tool ligand topology has been generated then i included ligand.itp file in topol.top file and pasted ligand.gro which is generated from PRODRG tool in protein.gro as suggested in tutorial but problem comes now<br>
while running editconf as follows warning bad box<br><br>editconf -f protein .gro -o box.gro -bt cubic -d 1.0<br><br><b>WARNING: Bad box in file protein.gro</b><br><br>Generated a cubic box 5.553 x 4.382 x 4.434<br>
Read 2053 atoms<br>Volume: 107.894 nm^3, corresponds to roughly 48500 electrons<br>No velocities found<br> system size : 5.553 4.382 4.434 (nm)<br> diameter : 6.093 (nm)<br> center : 0.068 -0.079 0.153 (nm)<br>
box vectors : 5.553 4.382 4.434 (nm)<br> box angles : 90.00 90.00 90.00 (degrees)<br> box volume : 107.89 (nm^3)<br> shift : 3.978 4.126 3.894 (nm)<br>new center : 4.047 4.047 4.047 (nm)<br>
new box vectors : 8.093 8.093 8.093 (nm)<br>new box angles : 90.00 90.00 90.00 (degrees)<br>new box volume : 530.06 (nm^3)<br><br><br>Actually this problem is already been raised from some one else in gromacs discussion list i tried to use that solution but it is not helping me<br>
<br>Can any body tell me where i am going wrong..<br><br>Thanks in advance<br><br>Nitin<br><br><br><span><br></span><br><span></span><br>