Single acetonitrile in water fails, while 3 work ok? Wild guess: is the
same acetonitrile lib being used in both cases? If not, I suggest close
comparison of leap output for building both models for clues.
Bill
On 1/24/19 11:27 AM, Debarati DasGupta wrote:
> 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?
>
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Received on Thu Jan 24 2019 - 12:30:02 PST
