Same 3-molecule file again. Maybe there's a clue in that to a user error
in setup?
Please run ambpdb on your single-solute prmtop/inpcrd, and let's see how
the resulting pdb looks.
On 1/25/19 8:00 AM, Debarati DasGupta wrote:
> this is the pdb of acetonitrile I used.
>
> ________________________________
> From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
> Sent: Friday, January 25, 2019 9:29 PM
> To: amber.ambermd.org
> Subject: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water)
>
> sander -O -i min_all.in -o allmin.out -p C3N_WAT.prmtop -c C3N_WAT.inpcrd -r allmin.rst -x allmin.crd -ref C3N_WAT.inpcrd
>
>
> Cannot understand at all what went wrong.
> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
>
> Backtrace for this error:
> #0 0x7FACEB01C6F7
> #1 0x7FACEB01CD3E
> #2 0x7FACEA52324F
> #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)
>
>
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Received on Fri Jan 25 2019 - 10:00:03 PST
