AMBER Archive (2004)

Subject: Re: Re: Re: Re: AMBER: a question about Van der waals radius

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Sat May 22 2004 - 10:01:28 CDT

I attached the gjf file of this cut system
181CYS of HIV-1 RT and nevirapine.

He Xiao

> I use DFT and also HF,too.There exits the repulsive reaction between them,
> while force field can not show this repulsive reaction.
> I just calculate the binding energy between protein and drug.
> I'm going to do a systemic study on this to show the E = E(R) profile.
> I just wanna to ask whether it may be a problem of Amber force field
> according to other users' experience, and whether it is a good project
> otherwise it will waste my time.
> Thank for anyone's suggestion.
>
> He Xiao
>
>
>I would need to know the van der Waals overlap in your system.
>Neither DFT nor HF should be used for systems with dispersion
>such as stacking, intercalation, etc.. They fail completely.
>cf. for example.
>Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations
>Hobza P, Sponer J
>Chemical Reviews
>99, 3247-3276, 1999
>Base stacking in cytosine dimer. A comparison of correlated ab initio
>calculations with three empirical potential models and density functional theory calculations
>Sponer J, Leszczynski J, Hobza P
>J. Comput. Chem.
>17, 841-850 1996
>
>If this is a pure H-bonding than the force field result would
>be strange, but I have never seen a failure of this kind for AMBER.
>It would be worth to analyze. What is the Lennard Jones component
>of your AMBER interaction energy?
>
>Best wishes, Jiri Sponer
>
>-------------------------------------------------------
>Jiri Sponer
>Institute of Biophysics
>Academy of Sciences of the Czech Republic
>Kralovopolska 135
>CZ-61265 Brno
>Czech Republic
>e-mail: sponer_at_ncbr.chemi.muni.cz
>fax: 420 5412 12179
>phone: 420 5415 17133
>http://www.ibp.cz/labs/LSDNA/
>http://ncbr.chemi.muni.cz
>Senior Wellcome Trust International Research Fellow for Biomedical Science
>--------------------------------------------------------
>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>__________ NOD32 1.770 (20040521) Information __________
>
>This message was checked by NOD32 Antivirus System.
>http://www.nod32.com

= = = = = = = = = = = = = = = = = = = =
                        

¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÖÂ
Àñ£¡
 
                                 
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Xiao He
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡hx_at_itcc.nju.edu.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-05-22


  • application/octet-stream attachment: cut.pdb

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu