AMBER Archive (2007)

Subject: AMBER: connecting a non standard residue to the rest of an enzyme

From: Boutheïna Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Fri Nov 23 2007 - 07:43:36 CST

Dear Amber users

I have created a non standard residue that is a part of an enzyme.
Now I have the file.lib, file.pdb, and the original pdb is original.pdb
The problem being that the Fe-SG-CB I cut out in file.pdb belong to
the same residue of the rest of cysteines CA-N-C-O. I have changed
the named of the all CYS connected to the non stadard part to CYX,
but xleap complains about name change in pdb file. Also
In xleap,
>loadoff file.lib
>original=loadpdb original.pdb
>edit original
This gives me twice the atoms in the file.pdb translated w respect to
each other + the cysteine atoms + new SG and CB atoms and H atoms.

How to overcome this duplicate pb, and how to connect properly my
bits of cysteines ie CA-N-CO to the non standard residue I cut out?

Thanks in advance for any help
Regards
______________________

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