[gmx-users] Re: genbox generating acetonitrile box with holes

[Diana Lousa]

Hi,

It seems to me that the holes are created by genbox because I don't have
them in the original solvent box. The intermediate box (outputed by trjconv)
with the protein solvated but not converted is difficult to analyze, because
the box doesn't have the right shape and of pbc issues, but it seems to me
that the holes are present in this box, i.e. I don't think they are an
artifact of trjconv.

Thanks for the help

Diana

On Sat, Nov 6, 2010 at 8:08 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Diana,
>
> Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
> reading, sorry. But are these holes created by genbox, or are they already
> present in the acn solven box? Have you already checked all intermediate
> structures?
>
> Cheers,
>
> Tsjerk
>
> On Nov 6, 2010 7:25 PM, "Diana Lousa" <dlousa at itqb.unl.pt> wrote:
>
> Hello,
>
> No, the hole don't correspond to parts of the protein sticking out on the
> other side. The protein is in the center of the box and the holes are not
> due to pbc issues.
>
>
> Diana
>
> On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
>> > > Hey, > > Do the holes match the parts of the protein sticking out on
>> the other side? > > Tsjerk ...
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>
>
> --
>
> Diana Lousa PhD student Protein Modeling Laboratory ITQB/UNL Oeiras,
> Portugal
>
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-- 
Diana Lousa
PhD student
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal
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