On Wed, Aug 28, 2013, sunyeping wrote:
>
> I am dealing with a protein with three chains and want to create the
> input file for amber MD. The protein has three disulfide bonds. They
> are:
>
> Chain A: residue 101 and 164
> Chain A: residue 203 and residue 259
> Chain B: residue 25 and residu2 80
>
> Using bond command in tleap works well for the first two disulfide bonds
> in chain A, but I don't know how to create the disulfide bonds in chain
> B. I tried:
>
> bond complex.25.SG complex.80.SG
>
> but it returns:
>
> Â bond complex.25.SG complex.80.SGÂ bond: Argument #1 is type String
> must be of type: [atom]usage:Â bond <atom1> <atom2> [order]
Use the "desc complex" command to find out what residue numbers go with
with residues.
...dac
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Received on Tue Aug 27 2013 - 19:30:02 PDT
