Re: [AMBER] bond command

From: David A Case <case.biomaps.rutgers.edu>
Date: Mon, 29 Jul 2013 09:29:01 -0400

On Sun, Jul 28, 2013, sunyeping.aliyun.com wrote:
>
> 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]

Use the "desc" command in tleap to find out exactly how LEaP is identifying
and numbering your residues. This depends a lot on exactly how the PDB file
looked, so it's best to check this for your particular situation.

...dac


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Received on Mon Jul 29 2013 - 06:30:02 PDT
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