AMBER Archive (2006)

Subject: Re: AMBER: Free energy perturbation in SANDER

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Thu Dec 14 2006 - 03:38:46 CST

Dear Yumi,

this article could be very useful to answer your question:

* *
        Hamelberg D, McCammon JA.
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15198616&query_hl=3&itool=pubmed_docsum>
        Related Articles,
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_DocSum&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15198616>
Links <javascript:PopUpMenu2_Set(Menu15198616);>
Abstract
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15198616&itool=iconabstr&query_hl=3&itool=pubmed_docsum>
        Standard free energy of releasing a localized water molecule from the
binding pockets of proteins: double-decoupling method.
J Am Chem Soc. 2004 Jun 23;126(24):7683-9.
PMID: 15198616 [PubMed - indexed for MEDLINE]

With regards,

Sergey

Yumi Nukusina wrote:
> Dear All
> I want to perform free energy perturbation calculation by SANDER module.
> I know it can be done using GIBBS module in AMBER7, but it's retired in
> AMBER8.
> SANDER module in AMBER8 can perform TI calculation but not free energy
> perturbation.
>
> If Free energy perturbation can be performed by SANDER module,
> Please tell me how to do?
>
> Thanks.
> Yumi
>
>
> ****************************************************************************
> **
> Yumi Nukushina
> E-mail : nuku-ym_at_09142002.mbox.media.kyoto-u.ac.jp
> ****************************************************************************
> ***
>
>
>
>
>
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