[gmx-users] Re: Dihedral Constraints

[bharat gupta]

Sorry for the last reply, I wrote turns with different sequences wrongly,
it's actually the turn with different dihedral constraints. I searched the
gromacs user list , where I found this link , regarding calculation of
dihedral energy of selected residues.  I want to know whether this method
would be useful ??

On Thu, Jun 14, 2012 at 4:16 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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>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
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>>
>>
>>
>>
>>
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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
>
>
>
>
>
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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
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