I am not quite sure I understood what the -refc input should look like from
the manual but here is what I tried. I created a file with the coordinates
of the atoms (15 atoms) on residue #16 (this molecule is centered in the
box)
1.1615000 -0.7975000 1.4650000
0.7655000 -0.1365000 0.1570000
-0.6935000 -0.1305000 -0.0820000
-1.0095000 0.2495000 -1.5080000
-0.5605000 1.5435000 -1.6610000
0.3385000 1.5005000 -1.9950000
1.3485000 -0.0155000 2.2020000
0.4545000 -1.5435000 1.8290000
2.0865000 -1.3615000 1.3510000
1.2125000 -0.5805000 -0.7330000
1.2355000 0.8425000 0.2530000
-1.1175000 0.5975000 0.6100000
-1.1825000 -1.1015000 -0.0000000
-0.4635000 -0.3905000 -2.2020000
-2.0865000 0.2365000 -1.6730000
Then I saved this and ran: sander -O -i qmtry.in -o qmtry.out -c c16.inpcrd
-p simbox.prmtop -ref c16.refc
This didn't change anything. I got the same output as before.
Also, just in case this is useful to anyone, I used a different software to
visualize the box and extract the residues that are within 3 A of residue
16. When I put the residue names in the qmmask instead of using a
distance-based criteria, sander was able to run successfully. This confirms
that the ambmask is what is causing the problem and not the actual box being
too small or the qm region being too large.
Thanks,
Aseel
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Thursday, January 19, 2017 10:34 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] ambmask issue
Shot in the dark: maybe because this is a distance-based mask you need
reference coordinates (-refc)?
-Dan
On Thu, Jan 19, 2017 at 10:21 AM Aseel Bala < <mailto:balaahme.msu.edu>
balaahme.msu.edu> wrote:
> Thank you for your suggestion. Unfortunately, that didn't do it
> either. I
>
> have played around with the ambmask quite a bit. Even selecting the
>
> individual atoms that make up residue #16 (so using '(.226-240<:3.0)')
>
> doesn't work either with sander.
>
>
>
> Thanks!
>
> Aseel
>
>
>
> -----Original Message-----
>
> From: David Case [ <mailto:david.case.rutgers.edu>
mailto:david.case.rutgers.edu]
>
> Sent: Thursday, January 19, 2017 8:26 AM
>
> To: AMBER Mailing List < <mailto:amber.ambermd.org> amber.ambermd.org>
>
> Subject: Re: [AMBER] ambmask issue
>
>
>
> On Wed, Jan 18, 2017, Aseel Bala wrote:
>
>
>
> > 1. Line 92: says Mask :16 <:3.0; matches 4530 atoms.
>
>
>
> This is what has to be fixed, since it leads to the other problems you
>
> mention.
>
>
>
> Wild guess: try removing the space between the "6" and the "<" character.
>
>
>
> ...dac
>
>
>
>
>
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