The CRYST1 line is odd to me, if you ambpdb the working model, does it have such a line 3x?
Bill
<div>-------- Original message --------</div><div>From: Debarati DasGupta <debarati_dasgupta.hotmail.com> </div><div>Date:01/25/2019 11:54 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] simple minimization error of a acetonitrile molecule in
water (TIP3P water) </div><div>
</div>The ambpdb generated a output like this....
CRYST1 25.514 26.069 25.400 90.00 90.00 90.00 P 1 1
ATOM 1 N1 C3N 1 13.602 11.328 13.525 1.00 0.00 N
ATOM 2 C2 C3N 1 13.093 12.228 13.104 1.00 0.00 C
ATOM 3 C3 C3N 1 12.573 13.423 12.503 1.00 0.00 C
ATOM 4 H4 C3N 1 12.762 13.469 11.483 1.00 0.00 H
ATOM 5 H5 C3N 1 11.489 13.480 12.567 1.00 0.00 H
ATOM 6 H6 C3N 1 13.022 14.282 13.017 1.00 0.00 H
TER 7 C3N 1
ATOM 7 O WAT 2 23.005 23.402 22.361 1.00 0.00 O
ATOM 8 H1 WAT 2 22.229 22.922 22.651 1.00 0.00 H
ATOM 9 H2 WAT 2 23.656 22.722 22.187 1.00 0.00 H
ATOM 10 O WAT 3 15.430 18.674 17.023 1.00 0.00 O
ATOM 11 H1 WAT 3 14.542 19.016 16.921 1.00 0.00 H
ATOM 12 H2 WAT 3 15.714 18.474 16.131 1.00 0.00 H
ATOM 13 O WAT 4 13.394 21.275 22.907 1.00 0.00 O
ATOM 14 H1 WAT 4 13.965 20.507 22.907 1.00 0.00 H
ATOM 15 H2 WAT 4 13.394 21.573 21.998 1.00 0.00 H
ATOM 16 O WAT 5 17.607 17.257 18.057 1.00 0.00 O
ATOM 17 H1 WAT 5 17.713 18.157 18.364 1.00 0.00 H
ATOM 18 H2 WAT 5 16.696 17.209 17.766 1.00 0.00 H
ATOM 19 O WAT 6 19.447 20.226 22.389 1.00 0.00 O
ATOM 20 H1 WAT 6 19.955 20.724 23.030 1.00 0.00 H
ATOM 21 H2 WAT 6 19.979 19.449 22.213 1.00 0.00 H
ATOM 22 O WAT 7 21.095 14.065 20.987 1.00 0.00 O
ATOM 23 H1 WAT 7 21.403 13.510 20.271 1.00 0.00 H
ATOM 24 H2 WAT 7 20.165 14.199 20.805 1.00 0.00 H
ATOM 25 O WAT 8 23.483 22.130 17.723 1.00 0.00 O
ATOM 26 H1 WAT 8 22.556 22.063 17.952 1.00 0.00 H
ATOM 27 H2 WAT 8 23.636 23.068 17.609 1.00 0.00 H
ATOM 28 O WAT 9 23.470 18.401 14.720 1.00 0.00 O
ATOM 29 H1 WAT 9 22.531 18.563 14.805 1.00 0.00 H
ATOM 30 H2 WAT 9 23.789 19.120 14.174 1.00 0.00 H
ATOM 31 O WAT 10 19.089 22.656 20.505 1.00 0.00 O
ATOM 32 H1 WAT 10 18.685 21.944 20.010 1.00 0.00 H
ATOM 33 H2 WAT 10 19.175 22.311 21.394 1.00 0.00 H
ATOM 34 O WAT 11 15.789 21.551 18.006 1.00 0.00 O
ATOM 35 H1 WAT 11 15.669 22.277 17.394 1.00 0.00 H
ATOM 36 H2 WAT 11 15.479 20.781 17.529 1.00 0.00 H
ATOM 37 O WAT 12 18.256 14.894 21.388 1.00 0.00 O
ATOM 38 H1 WAT 12 17.813 15.675 21.057 1.00 0.00 H
ATOM 39 H2 WAT 12 18.814 15.217 22.095 1.00 0.00 H
ATOM 40 O WAT 13 21.372 14.515 16.269 1.00 0.00 O
ATOM 41 H1 WAT 13 20.747 14.511 16.994 1.00 0.00 H
ATOM 42 H2 WAT 13 21.285 13.648 15.873 1.00 0.00 H
ATOM 43 O WAT 14 20.293 15.439 23.247 1.00 0.00 O
ATOM 44 H1 WAT 14 20.591 16.345 23.167 1.00 0.00 H
ATOM 45 H2 WAT 14 20.842 14.951 22.633 1.00 0.00 H
ATOM 46 O WAT 15 18.047 20.018 19.116 1.00 0.00 O
ATOM 47 H1 WAT 15 17.821 19.801 20.021 1.00 0.00 H
ATOM 48 H2 WAT 15 17.266 20.450 18.771 1.00 0.00 H
ATOM 49 O WAT 16 12.920 15.250 21.969 1.00 0.00 O
ATOM 50 H1 WAT 16 12.631 15.821 22.681 1.00 0.00 H
ATOM 51 H2 WAT 16 13.664 14.771 22.332 1.00 0.00 H
ATOM 52 O WAT 17 13.107 19.192 13.179 1.00 0.00 O
ATOM 53 H1 WAT 17 13.024 20.135 13.321 1.00 0.00 H
ATOM 54 H2 WAT 17 12.755 19.050 12.300 1.00 0.00 H
ATOM 55 O WAT 18 20.907 17.926 22.246 1.00 0.00 O
ATOM 56 H1 WAT 18 20.910 17.485 21.397 1.00 0.00 H
ATOM 57 H2 WAT 18 21.802 18.248 22.353 1.00 0.00 H
ATOM 58 O WAT 19 16.757 17.809 21.206 1.00 0.00 O
ATOM 59 H1 WAT 19 16.417 18.286 21.962 1.00 0.00 H
ATOM 60 H2 WAT 19 15.995 17.355 20.846 1.00 0.00 H
ATOM 61 O WAT 20 20.969 18.927 15.237 1.00 0.00 O
ATOM 62 H1 WAT 20 21.090 18.886 16.185 1.00 0.00 H
ATOM 63 H2 WAT 20 20.584 19.790 15.082 1.00 0.00 H
.
,
,
,
,
,
,
,
,
till 310 HOH molecules
So I have one ACN and 310 H2O molecules in ambpdb output.
Thanks
________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Friday, January 25, 2019 11:05 PM
To: amber.ambermd.org
Subject: Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water)
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 - 15:00:03 PST
