Re: [gmx-users] Dihedral angle PCA

2013-04-12 Thread baptista
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

Re: [gmx-users] Dihedral angle PCA

2013-04-12 Thread Thomas Evangelidis
> > > 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

Re: [gmx-users] Dihedral angle PCA

2013-04-12 Thread Mark Abraham
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

Re: [gmx-users] Dihedral angle PCA

2013-04-12 Thread Thomas Evangelidis
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

Re: [gmx-users] Dihedral angle PCA

2013-04-11 Thread anu chandra
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

Re: [gmx-users] Dihedral angle PCA

2013-04-11 Thread David van der Spoel
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

[gmx-users] Dihedral angle PCA

2013-04-09 Thread anu chandra
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

[gmx-users] Dihedral angle restraints

2012-12-04 Thread Antonia Mey
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

Re: [gmx-users] dihedral angle

2011-11-15 Thread Mark Abraham
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

[gmx-users] dihedral angle

2011-11-15 Thread Nilesh Dhumal
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

Re: [gmx-users] dihedral angle restraints

2009-04-02 Thread Justin A. Lemkul
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

Re: [gmx-users] dihedral angle restraints

2009-04-02 Thread Justin A. Lemkul
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 [

[gmx-users] dihedral angle restraints

2009-04-02 Thread Sandeep Pal
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

Re: [gmx-users] Dihedral angle in OPLS-AA force field

2006-09-11 Thread David van der Spoel
[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

Re: [gmx-users] Dihedral angle in OPLS-AA force field

2006-09-11 Thread David van der Spoel
[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

[gmx-users] Dihedral angle in OPLS-AA force field

2006-09-11 Thread alokjain
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