'If not' == "If that's not the issue." Same .lib file *should* be used.
Bill
On 1/24/19 12:23 PM, Bill Ross wrote:
> 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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>>
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Received on Thu Jan 24 2019 - 13:30:02 PST
