[gmx-users] Re: Dihedral Constraints

[bharat gupta]

Hi,

This query is related to my previous queries. I want to constraint the
psi/psi angle of the turn residue of my beta-hairpin , meaning that they
are allowed to move in certain range of psi/phi angle space.
Simultaneously, I want to freeze the movement of strand residues. This
procedure has to  be followed during minimization alone. From the previous
answers to my queries I understood how to constrain dihedral space, but I
don't know how to fix the movement of strand residues ?? ... any help will
be highly appreciated.

On Thu, Jun 14, 2012 at 4:24 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> 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
>>> 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
>>
>>
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
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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
>
>


-- 
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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