[gmx-users] Re: Dihedral Constraints

bharat gupta bharat.85.monu at gmail.com
Thu Jun 14 08:57:23 CEST 2012


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. 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. )


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
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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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