Ah ok, I thought that was too easy anyway. Somethings that I have heard
of, but never used myself, that might also help are the leap commands
"solvateCap" and "solvateShell" (probably one or the other is better
here). I believe one of these essentially just adds on additional layers
of solvent.
Brian
On Tue, Nov 8, 2011 at 2:04 PM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
>
> Hi Brian,
>
> thanks, no simulation is done yet. This is just a starting structure.
>
> Senthil
>
>
>
>
>
> By "not holding" do you mean it decreased during a constant pressure
> simulation? I think that's quite common behavior since the water boxes
> built by leap are generally quite low density (like 0.7 or something). An
> initial and rapid increase in density (i.e. decrease in volume) is pretty
> much par for the course with AMBER.
>
> Brian
>
>
> On Tue, Nov 8, 2011 at 1:18 PM, Senthil Natesan <sen.natesan.yahoo.com>
> wrote:
>
>
> >Hi Jan-Philip,
> >
> >Thanks for the response. I visually inspected the system and side chain
> of one residue is almost
> >out of the box.
> >
> >
> >Senthil
> >
> >
> >
> >Huhu,
> >
> >just to be sure that this is not an "issue of wrong perspective": did
> >you quantify the minimum distance between the complex and the box? How
> >big is it, if not 8 Angstrom?
> >
> >Jan-Philip
> >
> >On 11/08/2011 06:24 PM, Senthil Natesan wrote:
> >> Dear Amber Users,
> >>
> >> Greetings.
> >>
> >> I am trying to solvateOCT a protein-ligand complex, but the minimum
> distance between
> >> the complex and the solvent box edge seems to be not holding at the
> expected level (8 A)
> >> The protein-ligand complex is almost touching the box edge (pls see the
> attached image)
> >> though I get the proper solvation with solvateBox.
> >>
> >>
> >> The command used is
> >>
> >>
> >> solvateOct complex TIP3PBOX 8.0
> >>
> >> I am not sure what is wrong ? your suggestions/comments will be
> appreciated.
> >>
> >> thanks,
> >> Senthil Natesan
> >>
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Wright-Rieman Hall 101
> Graduate Program in Chemical Physics : 610 Taylor Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute
> appropriate address.
> _______________________________________________
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
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Received on Tue Nov 08 2011 - 12:00:02 PST
