[gmx-users] Re: Dihedral Constraints

[Mark Abraham]

On 14/06/2012 4:57 PM, bharat gupta wrote:
> I am not going to compare this with anything , I have to look for 
> sequences and their corresponding energies and select the lowest 
> scoring ones.

You can't compare total energies of different sequences and get a 
meaningful answer. What's the difference in energy between an apple and 
an orange mean? You can compare the average energy of an apple cut into 
pieces with the average energy of a whole apple, but that doesn't 
necessarily relate to the same quantity measured for an orange, either. 
There's a lot of work in measuring a decent *free* energy difference 
between some states.

> I request you to kindly elaborate on freezing some portion of the 
> protein. ( I am bit confused as in my case I am fixing the dihedral of 
> turn residues which means constraining them simultaneously I want to 
> freeze the other region of the protein. )

You need to read the link I gave last time and use "constraints" and 
"restraints" in the accepted GROMACS sense in order for people to be 
able to understand your meaning clearly. There are links there to the 
kind of methods that are available. I think you need to do some reading 
and thinking about those :-) If you lock down all the degrees of freedom 
then you can't measure anything relevant.

Mark

>
>
> On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 14/06/2012 4:38 PM, bharat gupta wrote:
>>     Thanks Sir for the reply... This question is related to my first
>>     query that if we constraint the dihedral of the turn residue how
>>     can we fix/freeze the movement of other residues.
>
>     http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
>
>
>
>>     As I am interested in only getting the energy of the hairpin when
>>     the turn residues are constrained within a particular phi psi
>>     angle range....
>
>     .. and with what are you going to compare those energies? And what
>     will that comparison mean?
>
>     Mark
>
>
>>
>>
>>     On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham
>>     <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>>         On 14/06/2012 12:04 PM, bharat gupta wrote:
>>
>>             Thanks for the reply . Is it possible to calculate the
>>             dihedral energy of certain residues, like in my case for
>>             turn residues ??.. How can that be done
>>
>>
>>         First, seek to define "dihedral energy"... Force fields are
>>         not parametrized such that parts of them are expected to
>>         correlate with observables.
>>
>>
>>
>>             This another question is regarding energy minimization.
>>             Suppose, I minimize the the protein solvated in water,
>>             the energy value that I get is for the whole system or
>>             for the protein alone. If it's for the system then how
>>             can I get the energy for the protein alone.
>>
>>
>>         You can define energy groups (see manual) to do this for the
>>         nonbonded contributions. Bonded contributions are easy to do
>>         in your case. Whether this energy is useful for anything is
>>         quite another matter.
>>
>>         Mark
>>
>>         -- 
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>>
>>
>>
>>     -- 
>>     Bharat
>>     Ph.D. Candidate
>>     Room No. : 7202A, 2nd Floor
>>     Biomolecular Engineering Laboratory
>>     Division of Chemical Engineering and Polymer Science
>>     Pusan National University
>>     Busan -609735
>>     South Korea
>>     Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>     Mobile no. - 010-5818-3680
>>     E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>
>>
>>
>
>
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>
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>
>
>

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