[AMBER] how to cut phosphodiester bond

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Tue, 8 Jun 2010 22:00:04 +0530 (IST)

Hello all

I have to cut phosphodiester bond for this i am using command in tleap:
   deleteBond atom1 atom2.
I have to cut bond between O3' of DC 4 and its position in PDB that I have lode
in tleap is 9th and P of DC 5 and its positon in PDB that I have load is 5th.
so I am giving command:
    deleteBond .R<DC 4>.A<O3' 9> .R<DC 5>.A<P 1>
is it correct command because I am getting output:
    deleteBond: Improper number of arguments!
    usage: deleteBond <atom1> <atom2>

Can anybody suggest how to do it.

With regard
Sangita Kachhap

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Received on Tue Jun 08 2010 - 10:00:03 PDT
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