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