[AMBER] bond command

From: <sunyeping.aliyun.com>
Date: Sun, 28 Jul 2013 12:12:14 +0800

Dear amber users,   I want to use bond command to build disufide bonds im structure. The structure has three chains: chain D, chian E and chain F. There are three disufide bonds in the structure:   one formed between residue 101 and residue 164 of chain D, one formed between 203 and 259 of chain D, and the other formed between resude 25 and 80 of chain E. I run the following command in tleap:   bond complex.101.SG complex.164.SGbond complex.203.SG complex.259.SGbond complex.10025.SG complex.10080.SG   the first two command seem OK, the the third get error message: bond: Argument #1 is type String must be of type: [atom]usage:  bond <atom1> <atom2> [order]   How tleap discrete residues in different chains? I have searched google for the problem, and one result says leap adds 10000 to the second chain. So I use "bond complex.10025.SG complex.10080.SG" for the second chain, chain E in my structure. But it doesn't work. Could anyone help me with that? the attached is the input pdb file.  

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Received on Sat Jul 27 2013 - 21:30:02 PDT
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