Hi all
I have a very small fundamental question.
I need to setup Linear Interaction Energy calculations for my system which is a protein +ligand.
my ligands are Acetonitrile, imidiazole and isopropanol. They are very weak binders.
For LIE I need to do two simulations, one with a probe alone in water and another with the probe bound to the protein.
When I setup a acetonitrile in water simulation, I get errors from Amber18.
My input file is Initial Minimization on Whole System
&cntrl
imin = 1,
igb = 0,
cut = 10.0,
maxcyc = 2000,
ncyc = 500,
ntb = 1,
/
Output errors are
sander -O -i min_all.in -o allmin.out -p C3N_WAT_box.prmtop -c C3N_WAT_box.inpcrd -r allmin.rst -x allmin.crd
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7F4955F8B6F7
#1 0x7F4955F8BD3E
#2 0x7F495549224F
#3 0x597E68 in __ew_recip_MOD_fill_charge_grid
#4 0x5989AC in __ew_recip_MOD_do_pmesh_kspace
#5 0x55DC6A in do_pme_recip_
#6 0x56091A in ewald_force_
#7 0x740673 in force_
#8 0x4EFCA9 in runmin_
#9 0x4DA58F in sander_
#10 0x4D13C5 in MAIN__ at multisander.F90:?
Segmentation fault (core dumped)
However when I use 3 acetonirile molecules and solvate it in TIP3P and create prmtop file and do the same step my simulation runs.
But I need to simulate one ligand molecule in water..
Where am I going wrong?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 24 2019 - 11:30:02 PST
