Use the free YASARA view. Then EDIT menu-> ADD BOND and pick the atoms you
want joined, select the bond type, and save.
Cheers,
Dean
On 1/27/12 12:28 PM, "James Starlight" <jmsstarlight.gmail.com> wrote:
>Dear Amber Users!
>
>
>I need to edit my pdb structure for further MD simulation.
>
>0- I've successful load my structure in the Xleap and run EDIT mode.
>
>
>1- I need to find special triplet motif ( e.g Thr-Leu-Gly) in my big
>protein.
>
>2- In this motiv I want to create new Covalent bond between 2 adjacent
>atoms ( e.g N atom in Gly and C atom in Thr) ( distance 1 A) and than
>make geometry optimisation of this new motif.
>
>
>
>How I could make it in Xleap?
>
>Thanks,
>
>James
>
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Received on Fri Jan 27 2012 - 13:00:02 PST
