Tleap gives new sequential numbering to residues.
It might occur that res.80 is not cystein in tleap.
Is your assignation correct?
Then, My suggestion is to check the original PDB
And newly created PDB in terms of residue number.
Best
IK
-----Original Message-----
From: sunyeping [mailto:sunyeping.aliyun.com]
Sent: Wednesday, August 28, 2013 10:43 AM
To: amber
Subject: [AMBER] problems with disulfide bond creation
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 - 19:00:03 PDT
