[gmx-users] problem in multichain protein solvation

Mark Abraham mark.abraham at anu.edu.au
Fri May 13 12:02:43 CEST 2011

On 13/05/11, Asmaa Elsheshiny  <pyaaea at leeds.ac.uk> wrote:
> 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.

> then,
> genbox -cs ffamber_tip3p.gro -cp rotated-box -p fragment -o sol
> when, I tried to visualize the protein using VMD I found the protein outside the box.

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


> Attached with this email, the topology and the structure file. So, what do you suggest?
> Regards,
> asmaa
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