Hi,
I would like to carry out dihedral pca with the dihedral angles (phi and
psi) of the peptide backbone. My question is how should I select my
dihedral angles?
I am using
mk_angndx -s *.tpr -n angle.ndx
The angle.ndx file so created contains all the dihedral angles I guess. How
should I select o
Hi,
I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has to be written in covar file .. According to manual it
says
-- Forwarded message --
From: bharat gupta
Date: Thu, Nov 21, 2013 at 4:52 PM
Subject: Re: Dihedral PCA
To: Discussion list for GROMACS users
Hi,
I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index fil
For extracting all the atoms involved in the phi-psi dihedral, you can use
make_ndx and select Mainchain group, then you can extract all the dihedrals
from the trajectory using the below command:
g_angle -f foo.xtc -s foo.tpr -n dangle.ndx -or dangle.trr -type dihedral
As described here: http://w
Hi Bipin
Thanks for the reply.
I have a small doubt won't selecting mainchain would also give owega rather
than only phi-psi angles?
Thanks
On Fri, Jan 2, 2015 at 6:14 PM, pratibha kapoor
wrote:
> Hi,
>
> I would like to carry out dihedral pca with the dihedral angles (phi and
> psi) of the pe
Yes, may be it will include omega too, but I am not sure. In that case, you
may select only the backbone atoms.
--
Thanks and Regards,
Bipin Singh
On Fri, Jan 2, 2015 at 7:36 PM, pratibha kapoor
wrote:
> Hi Bipin
>
> Thanks for the reply.
> I have a small doubt won'
Hi,
Please correct me if I am wrong but I believe that since torsion angle
omega is defined by 4 points in space namely Calpha (n) ,carbonyl carbon,
nitrogen, and calpha (n+1), omiting or including carbonyl oxygen (i.e.
using mainchain or backbone options) would not make a difference.
Secondly, is
I don't think the definition of omega dihedral which you have written is
correct,
--
Thanks and Regards,
Bipin Singh
On Sat, Jan 3, 2015 at 12:22 AM, pratibha kapoor
wrote:
> Hi,
>
> Please correct me if I am wrong but I believe that since torsion angle
> omega is d
I think it is... see http://en.wikipedia.org/wiki/Dihedral_angle
Cheers,
Tsjerk
On Fri, Jan 2, 2015 at 10:00 PM, bipin singh wrote:
> I don't think the definition of omega dihedral which you have written is
> correct,
>
>
> --
> Thanks and Regards,
> Bipin Singh
>
>
Even I have referred the previous link for its definition. But then, how
should I select my backbone phi-psi dihedral angles to proceed further with
dihedral pca?
Thanks
On Sat, Jan 3, 2015 at 12:22 AM, pratibha kapoor
wrote:
> Hi,
>
> Please correct me if I am wrong but I believe that since to
Please someone who has done dihedral pca can guide me to proceed further.
Waiting for reply.
On Sat, Jan 3, 2015 at 1:35 PM, pratibha kapoor
wrote:
> Even I have referred the previous link for its definition. But then, how
> should I select my backbone phi-psi dihedral angles to proceed further
Hi Pratibha
If you make the index file with only the backbone atoms the dangle.trr file
generated from
g_angle -f foo.xtc -s foo.tpr -n dangle.ndx -or dangle.trr -type dihedral
Gives you only the sine and cosine of backbone phi and psi dihedral angles
. You can check for it by converting your .t
Dear Gromacs users,
The documentation on Dihedral PCA analysis is confusing.
Firstly, the links are redirecting to the main gromacs page which does not
help because one needs to search for the specific commands from there.
Secondly, -s option does not work in step 2: invalid command line argu
Hi,
I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has to be written in covar file .. According to manual it
says
HI,
Sorry for posting this question again on the forum
I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has t
I think you might be referring to the 2010 version of the online manual (
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA), which is pretty
outdated. A lot of syntax seems to be changing fairly rapidly, so хрень
like this is to be expected. ;)
The current manual points to gmx angle, gmx c
Thanks Alex.
tried the new syntax, below the output of g_angle, which did not get any
easier... Хрень осталась...)))
Group 0 (UB_th=108.4_297.062f) has36 elements
Group 1 (UB_th=108.9_384.092f) has30 elements
Group 2 (UB_th=109.7_794.962f) has 6 elements
Group 3 (U
On 2/27/17 9:29 PM, Anna Vernon wrote:
Thanks Alex.
tried the new syntax, below the output of g_angle, which did not get any
easier... Хрень осталась...)))
Group 0 (UB_th=108.4_297.062f) has36 elements
Group 1 (UB_th=108.9_384.092f) has30 elements
Group 2 (UB_th=109.7_794
Thanks Justin,
but I did use this command, which is supposed to be dihedral:
g_angle -f h3_nowater.gro -n h3_ANGLE.ndx -or h3_ANGLE.trr -type dihedral
thanks
A
On 27/02/17 19:35, Justin Lemkul wrote:
On 2/27/17 9:29 PM, Anna Vernon wrote:
Thanks Alex.
tried the new syntax, below the ou
On 2/27/17 9:55 PM, Anna Vernon wrote:
Thanks Justin,
but I did use this command, which is supposed to be dihedral:
g_angle -f h3_nowater.gro -n h3_ANGLE.ndx -or h3_ANGLE.trr -type dihedral
Sure, but g_angle is only going to give you the options presented to it in the
index file. If thos
Thank you Justin,
that makes sense, thank you for help. However, I am struggling with the
rest, due to lacking documentation & examples. Like Alex said, this
web-page http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA is
outdated, but there is no new version of it available... Or at lea
Hi,
On Tue, Feb 28, 2017 at 5:51 AM Anna Vernon wrote:
> Thank you Justin,
>
> that makes sense, thank you for help. However, I am struggling with the
> rest, due to lacking documentation & examples. Like Alex said, this
> web-page http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA is
> o
Sorry for the delay, but I wanted to add a few points to this discussion
as I am doing my PhD in the group where dPCA was developed.
I hope these will clarify a little bit what's done in the tutorial and
why (took me a while to figure it out).
Obviously, it would be worth to rewrite my comments in
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