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

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

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

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
--
***********************************************************************
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455 E-mail: m.d.winn@dl.ac.uk *
* Fax: +44 1925 603825 Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
***********************************************************************

CCP4bb navigation

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

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

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