On Fri, 12 Apr 2013, Thomas Evangelidis wrote:
On 12 April 2013 07:51, anu chandra wrote:
Hi David,
Thanks for the reply. I have not tried yet. Since I didn’t find query about
the dihedral PCA in the mail list, I thought of confirm about the steps
mentioned in the web site.
Regarding the u
>
> > dPCA is
> > preferred in cases of peptides or intrinsically disordered proteins.
> >
>
> And even then a disordered mess can still be a disordered mess...
>
>
Very true!
--
==
Thomas Evangelidis
PhD student
University o
On Fri, Apr 12, 2013 at 11:28 AM, Thomas Evangelidis wrote:
> On 12 April 2013 07:51, anu chandra wrote:
>
> > Hi David,
> >
> > Thanks for the reply. I have not tried yet. Since I didn’t find query
> about
> > the dihedral PCA in the mail list, I thought of confirm about the steps
> > mentioned
On 12 April 2013 07:51, anu chandra wrote:
> Hi David,
>
> Thanks for the reply. I have not tried yet. Since I didn’t find query about
> the dihedral PCA in the mail list, I thought of confirm about the steps
> mentioned in the web site.
>
>
> Regarding the use of dihedral PCA, the protein with w
Hi David,
Thanks for the reply. I have not tried yet. Since I didn’t find query about
the dihedral PCA in the mail list, I thought of confirm about the steps
mentioned in the web site.
Regarding the use of dihedral PCA, the protein with which I am working
behave differently from others. From lit
On 2013-04-10 08:33, anu chandra wrote:
Dear Gromacs users,
I would like to do side-chain dihedral angle PCA for my protein. The
protein contains 293 residues. I came across an explanation about dihedral
PCA in gromcas website (
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA). Is it p
Dear Gromacs users,
I would like to do side-chain dihedral angle PCA for my protein. The
protein contains 293 residues. I came across an explanation about dihedral
PCA in gromcas website (
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA). Is it possible
to do side-chain dihedral PCA usin
Dear Gromacs users,
I have a question regarding position restraints on dihedral angles.
I would like to restrain the positions of phi and psi dihedral angles and on
top of that increase the potential barrier which needs to be over come in order
to go from one conformation to the next. (I.e. I w
On 16/11/2011 5:46 AM, Nilesh Dhumal wrote:
Hello,
I am trying to calculate the dihedral angle between four points.
I considered two planes (ABC& BCD) and calculate the dot products of two
normals (n1 and n2)to these plane.
theta=cos-1(n1.n2)
I compared theeta values of dihedral angle with a
Hello,
I am trying to calculate the dihedral angle between four points.
I considered two planes (ABC & BCD) and calculate the dot products of two
normals (n1 and n2)to these plane.
theta=cos-1(n1.n2)
I compared theeta values of dihedral angle with ampac and some values are
negative. I am geting
Justin A. Lemkul wrote:
Sandeep Pal wrote:
Hello,
I am trying to use dihedral angle restraints. I have added
; Dihedral angle restraints: No, Simple or Ensemble
dihre= yes
dihre-fc = 10
dihre-tau= 0
*Amendment* There is
Sandeep Pal wrote:
Hello,
I am trying to use dihedral angle restraints. I have added
; Dihedral angle restraints: No, Simple or Ensemble
dihre= yes
dihre-fc = 10
dihre-tau= 0
in my mdp file. My dihre.itp file looks like
[
Hello,
I am trying to use dihedral angle restraints. I have added
; Dihedral angle restraints: No, Simple or Ensemble
dihre = yes
dihre-fc = 10
dihre-tau = 0
in my mdp file. My dihre.itp file looks like
[ dihedral_restraints ]
; a
[EMAIL PROTECTED] wrote:
Dear All,
I have a basic question on Dihedral angle in OPLS-AA force field.
I read some of the papers related to development of OPLS force field where
they have different formula for calculating the torsion angle
I think that is Ryckaert-Bellemans function, but there is
[EMAIL PROTECTED] wrote:
Dear All,
I have a basic question on Dihedral angle in OPLS-AA force field.
I read some of the papers related to development of OPLS force field where
they have different formula for calculating the torsion angle
I think that is Ryckaert-Bellemans function, but there is
Dear All,
I have a basic question on Dihedral angle in OPLS-AA force field.
I read some of the papers related to development of OPLS force field where
they have different formula for calculating the torsion angle
I think that is Ryckaert-Bellemans function, but there is no separate term
for Impro
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