Thank you.
On Dec 11, 2017 3:54 PM, "Marcos Serrou do Amaral" <marcossamaral.gmail.com>
wrote:
> Dear Rana,
>
> Did you use parmed to double check that you have these bounds? If your
> answer is YES, you should ask for Chimera Group and you can go to next
> stage of your simulation.
>
> ---
> Marcos S.A.
>
>
> On Mon, Dec 11, 2017 at 8:00 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
> > Dear AMber users
> >
> > I follow the mcpb tutorial of heme metal containing protein. After that
> ran
> > the system for minimization and i got the .rst file then i use
> >
> > ambpdb -p b-h.prmtop -c min.rst > pdbauto.pdb
> >
> > to observe my system pdb in chimera visualization tool. Then I see That
> > chimera show only two bond one fe------NO and other fe------NA (porphyrin
> > nitrogen). It does not show the rest 3 porphyrin bond with FE and one
> > FE------HIS.
> > Is there anything wrong. Yes i know the bond information in the prmtop
> > file. And I can see bond after loading prmtop. But why chimera detect
> the
> > only 2 bond.
> > I also uploaded the image of system.
> > Kindly guide
> >
> > Thanks for yours Attentions.
> >
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> >
> >
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Received on Mon Dec 11 2017 - 07:00:04 PST
