[AMBER] creation of disulfide bonds

From: Beale, John <John.Beale.stlcop.edu>
Date: Fri, 8 Nov 2013 04:18:57 -0600

I am trying to use the "bond" command in xleap to create disulfide bonds in a protein. I use the following syntax on the example below:

bond cyx.117.SG cyx.129.SG

The bonding fails, and xleap gives me the following error message:

bond: Argument #1 is type String must be of type: [atom]

usage: bond <atom 1> <atom 2> [order]

Other information: the protein possesses two chains, A and B, and a few of the disulfide designations are the same in both chains.

Do I need to specify the chain designation with the "bond" command? If so, how do I do this?

I have followed this procedure successfully many times before. I can't figure out what I am doing wrong.



John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy
Saint Louis College of Pharmacy
4588 Parkview Place
Saint Louis, Missouri 63110-1088
Office: 314-446-8461
Cell: 314-315-0409
FAX: 314-446-8460

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Received on Fri Nov 08 2013 - 02:30:05 PST
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