[gmx-users] Protein ligand segmentation fault

[Justin A. Lemkul]

גדעון לפידות wrote:
> Hi all,
> 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 (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.
> When running the same protein with a similar ligand (pip2) who's 
> topology I have downloaded from the PDB website everything runs smoothly..
>  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.
> I'll be glad to provide further details to any one who think know what 
> might be wrong..

Please post an .mdp file for a run that is crashing.  Other general advice:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

Since the simulation runs for a short time, you should be able to watch the 
trajectory and see where it starts to fall apart.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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