[gmx-users] problem in multichain protein solvation

Tsjerk Wassenaar tsjerkw at gmail.com
Fri May 13 13:46:25 CEST 2011


> I tried to solvate an assembly of amyliod peptides (16 peptide), using
> editconf and genbox respectively as follow,
> editconf -f rotated.gro  -box  76 6 6 -center 0 0 0  -o rotated-box
> Nothing here does any rotation.

Well, it seems something that was rotated goes in... that seems fine.

> Sounds like the combination of your input coordinates, specification of the
> center and box sizes places the protein outside the box.

The specification of -center 0 0 0 will result in the center of
geometry of your chains to be placed at the origin. Your box will
start at the origin, so doing this by definition will place the
majority of your system outside of the box. Then again, if you process
it like you would for simulation, you will find it doesn't matter, as
there is no outside out of the box.

> So, what do you suggest?

Read more, in particular regarding periodic boundary conditions and go
on with the next step in your protocol.



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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