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

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Subject: Re: Molecular Dynamics for dummies.
From: Andrew Purkiss-Trew a {- dot -} purkiss {- at -} MAIL {- dot -} CRYST {- dot -} BBK {- dot -} AC {- dot -} UK
Date: 2008-07-03

Subject: Re: Molecular Dynamics for dummies.
From: Ed Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2008-07-03

GROMACS binaries are available for Macs

http://www.gromacs.org/content/view/32/100/

Afaic, GROMACS is user-friendly. There are good tutorials, and there is
even third-party GUI:

http://resal.atspace.com/grogui.htm

IMHO, the GUI is not much better than running Gromacs jobs from command
line, but it is rather helpful with visualization of energy trends, etc.

HTH.

On Thu, 2008-07-03 at 12:20 +0100, Martyn Winn wrote:
> Gromacs www.gromacs.org
>
> It is GPL. It can certainly handle metals, although as is always the
> case, you have to be careful in the choice of force field. It is fairly
> user friendly (by the standards of that field ;-). Not sure what the
> situation is for Macs but certainly runs well on Linux.
>
> Alternatives: charmm, amber, namd, etc etc
>
> Your suggested project is perfectly reasonable, but don't expect it to
> be a day's work ....
>
> HTH
> Martyn
>
>
> On Thu, 2008-07-03 at 11:30 +0100, David Briggs wrote:
> > 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
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /

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

Previous 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

Next message:
Subject: Re: Molecular Dynamics for dummies.
From: Andrew Purkiss-Trew a {- dot -} purkiss {- at -} MAIL {- dot -} CRYST {- dot -} BBK {- dot -} AC {- dot -} UK
Date: 2008-07-03