On 10/9/13 4:09 PM, Sainitin Donakonda wrote:
What functional significance does it have, if any? --- According to my
knowledge this reside is present in binding site.. and forms some hydrogen
bonds with ligand
Do you observe hydrogen bonds with the ligand?
What is the residue? -- *Glutam
Is that residue in a loop?
Gianluca
On Wed, 9 Oct 2013, Sainitin Donakonda wrote:
Hi all,
I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.
This analysis revealed particular residue in binding site of protein showed
quite
What functional significance does it have, if any? --- According to my
knowledge this reside is present in binding site.. and forms some hydrogen
bonds with ligand
What is the residue? -- *Glutamic Acid*
What did you measure - RMSF of the whole residue, just the backbone, just
C-alpha, etc? --*
On 10/9/13 3:29 PM, Sainitin Donakonda wrote:
Hi all,
I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.
This analysis revealed particular residue in binding site of protein showed
quite high fluctuation around 0.30 nm but o
Hi all,
I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.
This analysis revealed particular residue in binding site of protein showed
quite high fluctuation around 0.30 nm but other residues were in range of
0.15 to 0.20
Can a
Hi,
It should be able to find md.tpr unless your file is named something
else or you are issuing the command from other directory.
On Wed, Mar 13, 2013 at 9:31 AM, vansh wrote:
> to analyse the flexibility of the protein i used tge command
> g_rmsf -s md.tpr -f traj.xtc -oq
>
> but its showing t
to analyse the flexibility of the protein i used tge command
g_rmsf -s md.tpr -f traj.xtc -oq
but its showing that - can not open md.tpr file
as i am new to it cant figure it outany suggestions...
-
thanks in advance :)
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Hi Vandna,
You indicate that it should be in the directory where you issue to
command. It's not there. Maybe you used a different name for your
runs? Or you are in the wrong directory?
Cheers,
Tsjerk
On Sat, Feb 23, 2013 at 11:18 AM, vandna sharma wrote:
> as i want to analyse the local prote
as i want to analyse the local protein mobility, i used
g_rmsf -s md.tpr -f traj.xtc -oq
but its showing can not open file md.tpr...can anyone please suggest me from
where to get md.tpr file ???/
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On 8/16/12 10:13 AM, tdgrant1 wrote:
Dear all,
I have a 70 ns trajectory for which the last 60 ns appears to be
equilibrated. I'm attempting to create a plot of RMSF but I want to align
it to the equilibrated structure, not the starting structure. I first ran
g_rmsf using the starting struct
Dear all,
I have a 70 ns trajectory for which the last 60 ns appears to be
equilibrated. I'm attempting to create a plot of RMSF but I want to align
it to the equilibrated structure, not the starting structure. I first ran
g_rmsf using the starting structure as the reference structure over only
Hi Gurunath,
Each structure in the NMR ensemble is a fit to the experimental data.
Unlike an MD trajectory, you can not assume that the set of structures
is a proper sample from the Boltzmann distribution, and therefore, the
RMSF can not be expected to correspond to the RMSF of the system. Now,
on
Dear all,
I have a set of proteins(in pdb format) in which some are solved by X-ray
diffraction and some by NMR.
I have done the md simulation of these proteins using gromacs for 30ns [For
NMR structures, i have taken the first model as the starting structure]
Now, that i want to calculate the RMS
Il 15/04/2011 18:45, Alok Jain ha scritto:
Hi,
I am simulating a tetrameric protein in membrane. The simulation is
for 30ns. I wish to calculate RMSF for just one monomer (A).
I thought of doing this in two ways,
1. I input the residue numbers for the monomer A by creating an
index.ndx file to
Alok Jain wrote:
Hi,
I am simulating a tetrameric protein in membrane. The simulation is
for 30ns. I wish to calculate RMSF for just one monomer (A).
I thought of doing this in two ways,
1. I input the residue numbers for the monomer A by creating an
index.ndx file to calculate RMSF only for
Hi,
I am simulating a tetrameric protein in membrane. The simulation is
for 30ns. I wish to calculate RMSF for just one monomer (A).
I thought of doing this in two ways,
1. I input the residue numbers for the monomer A by creating an
index.ndx file to calculate RMSF only for the selected monomer
shiva birgani wrote:
Dear all
I want to analyze the mobility of residues in various conditions.
I need to know examining the RMSF is more useful or RMSD per residue?
That depends on your definition of "mobility." If you want to determine
fluctuations/flexibility, then RMSF will have meanin
Dear all
I want to analyze the mobility of residues in various conditions.
I need to know examining the RMSF is more useful or RMSD per residue?
Thanks in advance
Shiva
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Hi,
thank you all.
I have asked the question about RMSD because of the following reason:
I simulate a protein whose structure was determined by NMR only.
My simulation is quite long (2 microseconds) in the absence of a
ligand, present in the experimental structure file. During the course
of the s
Hi Andrei,
> If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
> structure, is a measure of the uncertanty in resolving the structure.
No, that's not what I said. You're saying that there's one structure
(the structure), but there is uncertainty in resolving it. That's not
the case
On Mar 16, 2010, at 10:24 AM, Mark Abraham wrote:
On 16/03/2010 8:17 PM, XAvier Periole wrote:
On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote:
Dear Mark and Tjerk,
Thank you for your comments.
If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
structure, is a measure of the
On 16/03/2010 8:17 PM, XAvier Periole wrote:
On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote:
Dear Mark and Tjerk,
Thank you for your comments.
If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
structure, is a measure of the uncertanty in resolving the structure.
Well, the "u
On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote:
Dear Mark and Tjerk,
Thank you for your comments.
If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
structure, is a measure of the uncertanty in resolving the structure.
Well, the "uncertainty of the NMR experiment" would be stro
Dear Mark and Tjerk,
Thank you for your comments.
If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
structure, is a measure of the uncertanty in resolving the structure.
Compared to this the RMSF of C-alpha computed from a MD trajectory
reflects the geometric fluctuations of the bac
On 15/03/2010 6:45 PM, Andrei Neamtu wrote:
Dear Mark,
Thank you very much for your response.
What I meant was to obtain a RMSF plot form PDB mediated on each
residue and to compare with a RMSF plot mediated on each residue
obtained from a MD trajectory.
I do not compare a frame from PDB with a
Hi Andrei,
You can do it this way. But do mind that the ensemble from NMR is not
meant to reflect the Boltzmann distribution. Rather it is meant to
provide a number of plausible solutions given the (positive)
restraints from the experiments and the force field used for the
refinement. This means t
Dear Mark,
Thank you very much for your response.
What I meant was to obtain a RMSF plot form PDB mediated on each
residue and to compare with a RMSF plot mediated on each residue
obtained from a MD trajectory.
I do not compare a frame from PDB with a frame from MD trajectory.
So, in the PDB file
On 14/03/2010 7:47 PM, Andrei Neamtu wrote:
Hi,
is there a rapid way to compute RMSF on an NMR ensemble from a PDB file?
Yes, but that's not your problem, it seems :-)
g_rmsf needs a .tpr file.
Not true. Inspect the lines in g_rmsf -h describing the file types
suitable for -f and -s. This
Hi,
is there a rapid way to compute RMSF on an NMR ensemble from a PDB file?
g_rmsf needs a .tpr file. This is OK with the MD trajectories but if I
want to compare MD ensemble one with the NMR RMSF ensemble
fluctuations from the original PDB this is not possible.
Thanks,
Andrei
--
gmx-users mai
Hi,
Actually, Justin is completely right (and I should've checked g_rmsf
-h). -od calculates the RMSD from the structure in the frame against
the structure in the topology file. This does not nullify the
statements regarding references for fitting and references for
deviations though :p
Cheers,
Pan Wu wrote:
Yes, I also think the *.tpr after -s maybe the reference state. However,
In this way, why in the manual it says like this?
"With the option -od the root mean square deviation with respect to
the reference structure is calculated"
What about without -od, should there be no ref
Hi Pan Wu,
There are two things to distinguish:
1. The reference structure used to remove translational and rotational
degrees of freedom
2. The reference against which the deviations (on a per atom base) are
calculated that are then squared, averaged and taken the root of (root
mean square fluct
Yes, I also think the *.tpr after -s maybe the reference state. However, In
this way, why in the manual it says like this?"With the option -od the
root mean square deviation with respect to the reference structure is
calculated"
What about without -od, should there be no reference structure or
Pan Wu wrote:
Hi everyone,
Thank you for answering my former questions, it really help me, the
new gmx-er a lot~
Here is another question about reference state of RMSF.
In the manual, it shows "g_rmsf computes the root mean square
fluctuation (RMSF, i.e. standard deviation) of at
Hi everyone,Thank you for answering my former questions, it really help
me, the new gmx-er a lot~
Here is another question about reference state of RMSF.
In the manual, it shows "g_rmsf computes the root mean square
fluctuation (RMSF, i.e. standard deviation) of atomic positions
after (
subarna thakur wrote:
Hello
I want to analyze the RMSF fluctuation of each residue of a protein
during a simulation run. I am giving the command
g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox
traj_avg.pdb. Then I am selecting the whole protein for the analysis. I
am getting
Hello
I want to analyze the RMSF fluctuation of each residue of a protein during a
simulation run. I am giving the command
g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox traj_avg.pdb.
Then I am selecting the whole protein for the analysis. I am getting the RMSF
per atom in the
Una Bjarnadottir wrote:
Dear users,
I have been trying to find information about the equation, which is used
in GROMACS to converts RMSF values to temperature factors. I know NAMD
uses:
B = (RMSF2 x 8π2)/3 and would like to know if the same is used in GROMACS.
Of course.
Cheers, Una
___
Dear users,
I have been trying to find information about the equation, which is used
in GROMACS to converts RMSF values to temperature factors. I know NAMD uses:
B = (RMSF2 x 8π2)/3 and would like to know if the same is used in GROMACS.
Cheers, Una
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