[gmx-users] problem in multichain protein solvation

Asmaa Elsheshiny pyaaea at leeds.ac.uk
Fri May 13 11:48:52 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
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.
Attached with this email, the topology and the structure file. So, what do you suggest?

More information about the gromacs.org_gmx-users mailing list