AMBER Archive (2004)

Subject: Re: AMBER: How to covalently bind a ligand to a residue?

From: Bimo Ario Tejo (bimo7_at_gmx.de)
Date: Fri Aug 06 2004 - 00:06:02 CDT

Hi Ozmer,

Use "bond" command in leap, then check your parm file by using "rdparm" to
make sure that particular bond is exist...

Regards,
Bimo

>
> Hi All,
>
> I wanna combine a sugar ligand to a Tyr residue from its O atom. I have
> prep
> file for the ligand from Glycam. I also modified Tyr by deleting the H of
> Tyr
> hydroxyl and formed a new prep file for Tyrosyl. Can anybody help me how
> to bond
> these covalently and form a new prep file for the ligand bound Tyrosyl
> group?
>
> Best,
>
> O.D.
>
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-- 
Bimo Ario Tejo
Computational Biology Unit (R.140)
Enzyme and Microbial Technology Laboratory 
Department of Biochemistry and Microbiology
Universiti Putra Malaysia
43400 Serdang
Malaysia
e-mail: bimo7_at_gmx.de
fax: +60-3-89430913

NEU: WLAN-Router für 0,- EUR* - auch für DSL-Wechsler!
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