Dear all,
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:
bond complex.25.SG complex.80.SG bond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]
Someone in amber mail list suggested that tleap add 10000 to the residue numbers of the second chain, so I tried:
bond complex.25.SG complex.80.SG
but the same error message appears. Would anyone help me with that? Thanks in advance!
Institute of Microbiology, Chinese Academy of Sciences
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Received on Tue Aug 27 2013 - 19:00:02 PDT
