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
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
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 differenc
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
whi
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_Restra
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
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 t
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
This another question is regarding energy minimization. Suppose, I minimize
the the protein solvated in water, the energy value that I get is for
On 6/13/12 9:44 PM, bharat gupta wrote:
Hi,
I wanted to simulate a beta-hairpin but with the dihedral angle of the turn
residues constrained as per my wish for eg phi angle should not 60 and psi
should be 90. Can anybody tell me how can I do this ??
http://www.gromacs.org/Documentation/How-
Hi,
I wanted to simulate a beta-hairpin but with the dihedral angle of the turn
residues constrained as per my wish for eg phi angle should not 60 and psi
should be 90. Can anybody tell me how can I do this ??
Regards
--
Bharat
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