[AMBER] Simulation setup for LIE

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Thu, 24 Jan 2019 19:27:04 +0000

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
  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?

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Received on Thu Jan 24 2019 - 11:30:02 PST
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