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.abra...@anu.edu.au
<mailto:mark.abra...@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.abra...@anu.edu.au <mailto:mark.abra...@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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
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