Dear yip,
>From my limited knowledge of amber.
Bonded cysteine is represents as CYX instead of CYS
Best,
Nitin Sharma
-----Original Message-----
From: Yip Yew Mun [mailto:yipy0005.gmail.com]
Sent: Sunday, February 23, 2014 8:53 PM
To: AMBER Mailing List
Subject: [AMBER] How to prepare the leap files for protein residues covalently bonded to ligand?
Importance: High
Hi, I have done antechamber and used gaussian to get the atomic charges on the covalently bonded ligand, which is to be bonded to a cysteine residue. However, when I run leap, it could not find angle parameters such as SH-ca-ca, SH-ca-ca, CT-SH-ca. However, I'm totally unable to generate the prep file parameters containing them, as the atom names of the cysteine moiety in my antechamber files are not named like the actual cysteine residue. What can I do?
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences Nanyang Technological University
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Received on Sun Feb 23 2014 - 11:00:03 PST
