On Wed, Sep 14, 2011, Fabrício Bracht wrote:
> Hi. I am trying to make a bond between two atoms using xleap as part
> of a parameterization process for a new aminoacid residue. I have both
> my protein and new residue in the same pdb file. I am using ambertools
> 1.5. Every time I hit the bond command, It gives out an error message.
> Here are some details on my atom numbering.
> The first atom is Atom number 1519. It ts a carbonyl carbon (C) in
> residue 104. This should be linked to atom number 59082 wihin residue
> 3178 (N1). I've called the molecule in leap "mic".
bond mic.104.C mic.3178.N1
Note that you can use the "desc" command to see if each individual part is
what you want, e.g.
desc mic.104.C
should show details of that atom, including what it is currently bonded to.
After the "bond" command, repeating the desc command should show the new bond.
...good luck...dac
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Received on Thu Sep 15 2011 - 12:00:04 PDT
