can try
-ref c16.inpcrd
Hai
On Thu, Jan 19, 2017 at 1:16 PM, Aseel Bala <balaahme.msu.edu> wrote:
> 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
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > _______________________________________________
>
> >
>
> > AMBER mailing list
>
> >
>
> > <mailto:AMBER.ambermd.org> AMBER.ambermd.org
>
> >
>
> > <http://lists.ambermd.org/mailman/listinfo/amber>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > _______________________________________________
>
> >
>
> > AMBER mailing list
>
> >
>
> > <mailto:AMBER.ambermd.org> AMBER.ambermd.org
>
> >
>
> > <http://lists.ambermd.org/mailman/listinfo/amber>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
> >
>
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>
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Received on Thu Jan 19 2017 - 11:00:02 PST
