[ccp4bb] Molecular Dynamics for dummies.

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: FW: .getTwoTheta() in DiffractionImage library
From: Georg Zocher georg {- dot -} zocher {- at -} BESSY {- dot -} DE
Date: 2008-07-03

Next message:
Subject: Re: Molecular Dynamics for dummies.
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-07-03

Subject: Molecular Dynamics for dummies.
From: David Briggs drdavidcbriggs {- at -} GMAIL {- dot -} COM
Date: 2008-07-03

Hi everyone.

I have a slightly off topic question I hope someone can help with.

I have a structure of a wild type domain, which binds metal ions.
Certain mutations in chelating residues cause changes in the apparent
affinity for said metal ions.

As I have (so far) failed to crystallise the mutant, I would like to
do some molecular dynamics in a water box, (with afore mentioned
mutations) to get a handle on the origin of the change in metal ion
affinity.

Does anyone know of a suitable package which:

a) is open source, or basically free to academics
b) allows inclusion of metal ions
c) gives an understandable and interpretable output, in terms of
changes in energy, etc.
d) Preferably runs on mac, (although I do have access to linux as well.)

Am I asking for the moon on a stick?

Looking forward to your responses.

Regards,

Dave
--
============================
David C. Briggs PhD
Father & Crystallographer
http://www.dbriggs.talktalk.net
AIM ID: dbassophile
============================

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: FW: .getTwoTheta() in DiffractionImage library
From: Georg Zocher georg {- dot -} zocher {- at -} BESSY {- dot -} DE
Date: 2008-07-03

Next message:
Subject: Re: Molecular Dynamics for dummies.
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-07-03