On 13/05/11, Asmaa Elsheshiny <pya...@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. Mark > > Attached with this email, the topology and the structure file. So, what do > you suggest? > Regards, > asmaa > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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