[gmx-users] Re: Dihedral Constraints
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.
> 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?
> 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
>> First, seek to define "dihedral energy"... Force fields are not
>> parametrized such that parts of them are expected to correlate with
>>> 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.
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