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

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Nov 6 21:24:25 CET 2010

Hi Diana,

Does it also happen if you solvate the box without the protein? And are the
holes close to the protein or just anywhere? And what makes it difficult to
analyze the structure output by genbox directly, perhaps specifying that the
output be .pdb? It's what I usually do.



On Nov 6, 2010 9:15 PM, "Diana Lousa" <dlousa at itqb.unl.pt> wrote:


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


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

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