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: Ed Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2008-07-03

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Subject: Off-topic: ELIXIR Letter of Support
From: Miguel_Ortiz-Lombardía ibdeno {- at -} GMAIL {- dot -} COM
Date: 2008-07-03

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

Just a word of warning regarding metals in macromolecular simulation.
There is no 'good' way of modeling protein-metal interactions in many
cases. Some metal ions are very polarizable (Ca 2+ being one example)
and the simple mechanics used in protein simulation don't allow for
this. Even using a polarizable forcefield is unlikely to give accurate
answers due to the complex nature of the atomic orbitals ï»¿in many metal
ions when compared to protein atoms (mainly due to the addition of
d-orbitals to the mix). So, Na+, Mg2+ are generally OK, Ca2+, Fe, Mn,
etc. are much more tricky, especially in a quick and dirty simulation.

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

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

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

Next message:
Subject: Off-topic: ELIXIR Letter of Support
From: Miguel_Ortiz-Lombardía ibdeno {- at -} GMAIL {- dot -} COM
Date: 2008-07-03