Hi. Is there a problem in making the complete box (protein + ethanol + water)
with packmol and then setting the PBC.
Amin.
> Ok This I can test. But I dought whether this will make the correct size of
> box since I am using 3 ethanol molecules for each 10000 water molecules.
>
> On Mon, Dec 17, 2012 at 12:14 AM, Aron Broom <broomsday.gmail.com> wrote:
>
>> no, that's not what I'm saying. If you solvate like so:
>>
>> "solvateBox yourUnit TIP3PBOX 0.0 1.0"
>>
>> It will make a box where the closest distance between a water and your
>> protein or ethanol is 1.0 angstroms, and where there is a 0.0 angstrom
>> distance from these to the edge of the periodic box. If your ethanols
>> already loosely define the box, then that will be good, no?
>>
>> On Mon, Dec 17, 2012 at 1:07 AM, Chinthaka Ratnaweera <cnr88.msstate.edu
>> >wrote:
>>
>> > Thanks, But I think I need the periodic boundary conditions for the
>> > simulation. Just adding ethanols will not create periodic box.
>> >
>> > On Sun, Dec 16, 2012 at 11:58 PM, Aron Broom <broomsday.gmail.com>
>> wrote:
>> >
>> > > but if the ethanols are already making up roughly the box size you
>> want,
>> > > can't you just give no boundary, or close to it?
>> > >
>> > > On Mon, Dec 17, 2012 at 12:14 AM, Chinthaka Ratnaweera <
>> > cnr88.msstate.edu
>> > > >wrote:
>> > >
>> > > > I have to use certain concentration of ethanol/water mixture for my
>> > > protein
>> > > > model. I couldn't find ethanol solvatebox in amber. so I randomly
>> added
>> > > > desired number of ethanol molecules to a given box size (using
>> > packmol).
>> > > > But now the problem is when I add water solvatebox (tip3p), ethanols
>> > also
>> > > > consider as a part of the solute and count the distance for
>> boundaries
>> > > from
>> > > > ethanol molecules making the box size much larger which I do not
>> want.
>> > > > Appreciate if any one can guide me to solve this problem. Thank you.
>> > > >
>> > > > Chinthaka
>> > > > _______________________________________________
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>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Aron Broom M.Sc
>> > > PhD Student
>> > > Department of Chemistry
>> > > University of Waterloo
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> >
>> >
>> >
>> > --
>> > Chinthaka Nadun Ratnaweera
>> > Hand Lab Rm 1126
>> > Mississippi State University
>> > 310 Presidents Circle
>> > Starkville, MS 39762
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Dec 17 2012 - 03:30:03 PST
