<div dir="rtl"><div dir="ltr">Hi all, <br>I have been trying to run a protein ligand simulation in water using Gromacs version 4.0.7 and GROMOS 53a6 ff. My protein is about 250 aa and my ligand is pip3 (<span class="tl"></span><font size="2">Phosphatidylinositol (3,4,5)-trisphosphate) which I have constructed using PRODRG (using EM and full charges option). I have tried running the simulation several times under different conditions and every time the simulation crashed around the first few ps of MD giving a segmentation fault. I have tried coupling the temp and pressure of the ligand to the solvent and other times to the protein, changing the partial charges of the ligand using common GROMOS FF parametes.<br>
When running the same protein with a similar ligand (pip2) who's topology I have downloaded from the PDB website everything runs smoothly..<br> when running the protein and ligand in separate simulations they both run fine. I have also tried taking frames from the ligand and protein separate simulations and then placing them in the same box and still the simulation crashes. I have gone through Justin's tutorial on protein ligand simulations but to no avail. <br>
I'll be glad to provide further details to any one who think know what might be wrong..<br>Thanks,<br>Gideon <br></font><h3 style="font-weight: normal;" class="r"> </h3></div></div>