On 11/12/13 8:33 AM, bharat gupta wrote:
Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.
Because that's not the function of g_analyze. Use trjconv -dump with a suitable
index file (from g_select).
-Justin
On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/11/13 6:56 PM, bharat gupta wrote:
Hi,
I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?
Start with g_select -select 'help all' and see what you can determine.
Such selections are rather straightforward and have been explained several
times on the list. If you need help, show us what you're doing and
describe why it isn't what you want. It will ultimately save a lot of time.
-Justin
On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta <bharat.85.m...@gmail.com>
wrote:
Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-
https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg
Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does
then
the average file or its graph tells ??
On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/11/13 4:06 AM, bharat gupta wrote:
In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and
plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives
7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-
std. dev. relative deviation of
standard --------- cumulants from
those
of
set average deviation sqrt(n-1) a Gaussian
distribition
cum. 3 cum. 4
SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.062 0.163
SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.495 0.153
https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png
Here's the link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
Neither of these files produce output that corresponds to the PNG
image
above. Both files have values in 6-9 H-bond range and thus agree with
the
g_analyze output, which I can reproduce. I suspect you're somehow
getting
your files mixed up.
-Justin
On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta <
bharat.85.m...@gmail.com>
wrote:
thank you informing about g_rdf...
Is it possible to dump the structure with those average water
molecules
interacting with the residues. I generated the hbond.log file which
gives
the details but I need to generate a figure for this ??
On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 11/10/13 8:38 PM, bharat gupta wrote:
But trjorder can be used to calculate the hydration layer or shell
around
residues ... Right ??
Yes, but I also tend to think that integrating an RDF is also a
more
straightforward way of doing that. With trjorder, you set some
arbitrary
cutoff that may or may not be an informed decision - with an RDF it
is
clear where the hydration layers are.
-Justin
On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 11/10/13 8:30 PM, bharat gupta wrote:
Thanks for your reply. I was missing the scientific notation
part.
Now
everything is fine.
Regarding trjorder, it doesn't measure h-bonds but gives the water
nearest
to protein.
I wouldn't try to draw any sort of comparison between the
output
of
trjorder and g_hbond. If you want to measure H-bonds, there's
only
one
tool for that.
-Justin
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Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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