Hi Nitin,
CYX is for cysteines that form disulfite bridges. I'm not sure whether it
can be used in my case to bond with a ligand instead. Have you tried it
before?
With regards,
Yew Mun
On Mon, Feb 24, 2014 at 2:31 AM, Nitin Sharma <sharmanitin.nus.edu.sg>wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards
Yip Yew Mun
Graduate, Masters
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 23 2014 - 18:00:02 PST
