AMBER Archive (2006)

Subject: AMBER: Steered molecular dynamics with Amber 8.0

From: a a (
Date: Tue Oct 10 2006 - 04:44:56 CDT

Dear All,

It seems to me that I cannot do the steered molecular dynamics calculations
without an external script, in order to run this calculations with Amber

I could like to ask if you could kindly share this powerful script with me,
or if you know the source of this script, could you please kindly let me
know too?

Best regards and many thanks in advanced,


>From: "a a" <>
>Subject: AMBER: Potential of Mean Force calculation or Steered molecular
>dynamics Date: Mon, 09 Oct 2006 14:07:25 +0800
>Dear Feng and Ambers,
>Thank you very much for your suggestions.
>Can I run Potential of Mean Force calculation (or Steered molecular
>dynamics) with amber 8.0? If yes, I will try to so. If the answer is not,
>could you please kindly suggest how can I do this type of calculations?
>Best regards,
>>From: Feng X Zhou <>
>>Subject: Re: AMBER: RMSD: is it related to flexibility?
>>Date: Fri, 6 Oct 2006 11:28:36 -0500
>> Is it true the flexibility of the loop is related to the releasing
>>process of the metabolite, i.e., the transition state energy is lower
>>for the mutated enzyme due to a more adaptable loop to accmodate the
>>distorted state when the metaboliote is coming out of the protein?
>> This is the impression I got reading your email... and if this is
>>the speculation you are working on, MD might be a right tool compared to
>>DOCK since it can do dynamics ... Have you considered doing a Potential
>>of Mean Force calculation (or Steered molecular dynamics) to calculate the
>>binding energy & transition state energy? This way the binding
>>constant and transition state barrier can both be estimated, along with a
>>conformation comparison to see what exactly allowed the mutant to be more
>>adaptive to distortion - that is if the MD simulation is accurate and
>>realistic enough (the longer than better)
>>Just 2 pennies -:)
>>-Feng Zhou
>>Subject: Re: AMBER: RMSD: is it related to flexibility?
>>From: Gustavo Seabra (
>>Date: Thu Oct 05 2006 - 11:08:05 CDT
>>Previous message: Thomas Cheatham: "Re: AMBER: ptraj hbond analysis
>>In reply to: a a: "Re: AMBER: RMSD: is it related to flexibility?"
>>Next in thread: a a: "Re: AMBER: RMSD: is it related to flexibility?"
>>Next in thread: Bill Ross: "Re: AMBER: mdcrd file"
>>Reply: a a: "Re: AMBER: RMSD: is it related to flexibility?"
>>Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>If all you want is to compare flexibilities, it may be a beter idea to
>>define a couple of characteristic internal distances and monitor them
>>in time. For a better description of the method, take a look at:
>>"Sulfide Binding Hemoglobins: Effects of Mutations on Active Site
>>Fernandez-Alberti et al. Biophys. J. vol. 91, p.1698 (2006)
>>Best wishes,
>>Gustavo Seabra.
>>On 10/5/06, a a <> wrote:
>> > Dear David,
>> >
>> > Thank you very much for your comments. The following is the
>> > work done previously. Both the wild type and mutated proteins form a
>> > covalent complex with a drug. They both modified the drug to a
>> > Experimentally, we measured the metabolite concentration over the time,
>> > and found mutant one produce metabolite ten times faster than the wild
>> > We originally expected that it is due to different binding affinity of
>> > drug, but finally we found the binding affinities for these two
>> > the drug are the same both experimentally and theoretically (docking).
>> > it is well documented that the rate for these protein to release the
>> > metabolite is a function of a flexibility of a loop on these proteins
>> > loop is mutated). Thus, we try to see if the mutation change the
>> > flexibility of the loop theoretically, so as to explain the increased
>> >
>> > Follow the tutorial on the web, I carried out minimization, equilibrium
>> > a production 1-ns MD with sander for these two proteins, and double
>> > that the potential energies are stable at the production period. This
>> > the preliminary result that we got. The RMSD (reference to a PDB file)
>> > the loop of the wild type protein in average is 2.0, but 3.0 for the
>> > one. The RMSD vs time plot shown that the RMSD increase from zero and
>> > reach stable (~ 4 A) at ~300 ps for the wild type and ~200 ps for the
>> > mutant. Is the difference in terms of RMSD (1-2 A) and time to reach
>> > (100 ps) significant enough for drawing any conclusions?
>> >
>> > If not, could you mind to suggest the best way to model the release
>> > metabolite B from these two proteins?
>> >
>> > I am new to MD calculations, just learn it several months ago from the
>> > websites, your professional suggestions are valuable to me. Many thanks
>> > advanced.
>> >
>> > Best regards,
>> >
>> > Ann
>> >
>> > >From: "David A. Case" <>
>> > >Reply-To:
>> > >To:
>> > >Subject: Re: AMBER: RMSD: is it related to flexibility?
>> > >Date: Wed, 4 Oct 2006 08:08:32 -0700
>> > >
>> > >On Wed, Oct 04, 2006, a a wrote:
>> > > >
>> > > > I got two protein structures with different performance on the loop
>> > > > mobilitiy, one of them move very fast, another one is about 10 time
>> > > > flexible, based on our experimental data.
>> > >
>> > >The answer probably depends on what kind of experimental data one is
>> > >talking
>> > >about here; that will effectively determine what is being measured and
>> > >represented as "flexibility". And that, in turn, will help decide what
>> > >sorts
>> > >of calculations might be relevant.
>> > >
>> > >...regards...dac
>> > >
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