That command is not obsolete. It will add the water and the box
information. The box info is placed in the coordinate file. Dave just said
that the box information in the prmtop file is not used.
On Wed, Aug 4, 2021, 12:31 AM James Kress <jimkress_58.kressworks.org>
wrote:
> Are you saying that this command is wrong/ obsolete?
>
> >> solvateOct protein TIP3PBOX 10
>
> Jim
>
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> -----Original Message-----
> From: David A Case <dacase.chem.rutgers.edu>
> Sent: Tuesday, August 03, 2021 9:08 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] SolvateOct box volume and cubic box information
>
> On Wed, Aug 04, 2021, Umesh Roy wrote:
>
> >> solvateOct protein TIP3PBOX 10
> >
> >%FLAG BOX_DIMENSIONS
> >%FORMAT(5E16.8)
> > 1.09471219E+02 *6.31036082E+01 6.31036082E+01 6.31036082E+01*
> >%FLAG RADIUS_SET
>
> Two points here:
>
> First: since the box size (often) changes during a simulation, it should
> never have been put into the prmtop file -- the prmtop file is for things
> that don't change. So, the information in the prmtop file is ignored: box
> information is always taken from the coordinate file. (The information is
> still there for backwards compatibility with *very* old files.)
>
> (Second: however, the 109.47 value above did originally indicate that this
> was a truncated octahedron, and not a cubic box.)
>
> >* Box X = 63.104 Box Y = 63.104 Box Z = 63.104*
> > Alpha = 109.471 Beta = 109.471 Gamma = 109.471
>
> Above is the box information taken from the input coordinate file.
>
> >This means that box information saved in the topology file is used for
> >the subsequent/production run.
>
> This is not correct. As noted above, any box information in the prmtop
> file
> is ignored.
>
> ...hope this helps....dac
>
>
>
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Received on Wed Aug 04 2021 - 04:30:03 PDT
