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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
