Message: 1
Date: Tue, 26 Aug 2008 15:38:56 +0530 (IST)
From: [EMAIL PROTECTED]
Subject: [gmx-users] g_hbond output analysis
To: gmx-users@gromacs.org
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Content-Type: text/plain;charset=iso-8859-1
hi
i used the -num option for g_hbond run. since i new
--
Message: 4
Date: Sun, 18 May 2008 00:50:30 +0200
From: Xavier Periole [EMAIL PROTECTED]
Subject: Re: [gmx-users] g_hbond distance distribution problem
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain
Dechang Li wrote:
--
Message: 4
Date: Sun, 18 May 2008 00:50:30 +0200
From: Xavier Periole [EMAIL PROTECTED]
Subject: Re: [gmx-users] g_hbond distance distribution problem
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED
Dear all,
I used command g_hbond to calculated the distance distribution of hbonds
in my system. There are two columns in the file hbdist.xvg, as showed follow:
@title Hydrogen Bond Distribution
@xaxis label Hydrogen - Acceptor Distance (nm)
@yaxis label
@TYPE xy
0.0025
Dechang Li wrote:
Dear all,
I used command g_hbond to calculated the distance distribution of
hbonds
in my system. There are two columns in the file hbdist.xvg, as showed
follow:
@title Hydrogen Bond Distribution
@xaxis label Hydrogen - Acceptor Distance (nm)
@yaxis label
Hi all:
I´m using gromacs version 3.3.2 and a box type truncated octahedron.
I need to analyze hydrogen bonds with solvent (water)insertion but -ins
option of g_hbond is broken... What should I do?
I´ve allready tried to analyze my trayectory file (maked with 3.3.2) with
gromacs version 3.1.4 but
Michel Cuendet wrote:
Hi,
I'm trying to look at contacts between two proteins at the individual
atom level. I have a bunch of analysis scripts that use the .xpm file
and work for h-bonds, so I wanted to use the output of g_hbond 3.3.2
again with the option -contact. But:
g_hbond -hbn -hbm
Hi,
I'm trying to look at contacts between two proteins at the individual
atom level. I have a bunch of analysis scripts that use the .xpm file
and work for h-bonds, so I wanted to use the output of g_hbond 3.3.2
again with the option -contact. But:
g_hbond -hbn -hbm -num -contact -r 0.4
Michel Cuendet wrote:
Hi,
I'm trying to look at contacts between two proteins at the individual
atom level. I have a bunch of analysis scripts that use the .xpm file
and work for h-bonds, so I wanted to use the output of g_hbond 3.3.2
again with the option -contact. But:
g_hbond -hbn -hbm
Michel Cuendet wrote:
Hi,
I'm trying to look at contacts between two proteins at the individual
atom level. I have a bunch of analysis scripts that use the .xpm file
and work for h-bonds, so I wanted to use the output of g_hbond 3.3.2
again with the option -contact. But:
g_hbond -hbn -hbm
Michel Cuendet wrote:
Hi,
I'm trying to look at contacts between two proteins at the individual
atom level. I have a bunch of analysis scripts that use the .xpm file
and work for h-bonds, so I wanted to use the output of g_hbond 3.3.2
again with the option -contact. But:
g_hbond -hbn -hbm
Michel Cuendet wrote:
Hi,
I'm trying to look at contacts between two proteins at the individual
atom level. I have a bunch of analysis scripts that use the .xpm file
and work for h-bonds, so I wanted to use the output of g_hbond 3.3.2
again with the option -contact. But:
g_hbond -hbn -hbm
Dear David,
Thanks for your concern.
i am using g_hbond (After vacuum md, just for one step)
Command with options is
g_hbond -f *.pdb -s *.tpr -num *_num.xvg -hx *_hbhelix.xvg
and when i compare the result of v 3.3.1 and v 3.14, i found there is
difference in *_hbhelix.xvg.
Even for standard
Dear All,
I found there is some problem with version 3.3 to g_hbond command. Earlier
i was using version 3.14, and when i was using g_hbond(v3.14) i found
correct distribution of hydrogen bond pattern (i.e., n-n+1,n-n+2, n-n+3 so
on).
But when i use g_hbond (v3.3) then i found it only gives
Dear All,
I found there is some problem with version 3.3 to g_hbond command. Earlier
i was using version 3.14, and when i was using g_hbond(v3.14) i found
correct distribution of hydrogen bond pattern (i.e., n-n+1,n-n+2, n-n+3 so
on).
But when i use g_hbond (v3.3) then i found it only gives
Anil Kumar wrote:
Dear All,
I found there is some problem with version 3.3 to g_hbond command. Earlier
i was using version 3.14, and when i was using g_hbond(v3.14) i found
correct distribution of hydrogen bond pattern (i.e., n-n+1,n-n+2, n-n+3 so
on).
But when i use g_hbond (v3.3) then i
Dear Users,
I have done clustering of equilibrium ensemble of octa-alanine model
system, and when i was trying to find the no. of hydrogen bonds for each
cluster, i found different result with different versions.
Is there some bug to version 3.3 in comparison of version 3.14 or am i
doing the
Dear all users,
I want to analyze Hydrogen-bond among water molecules using g_hbond
command. We use periodic boundary conditions in the simulation box.
The question is: I don't know whether this g_hbond tool considers the
periodic boundary conditions, that is,
whether this tool
wangcl wrote:
Dear all users,
I want to analyze Hydrogen-bond among water molecules using g_hbond
command. We use periodic boundary conditions in the simulation box.
The question is: I don't know whether this g_hbond tool considers the
periodic boundary conditions, that is,
whether
Dear all,
I have two moleculars in the .trr. I want to use g_hbond to analyze the
hydrogen bonds between them. Can g_hbond analyze the hydrogen bonds between
two moleculars associated by a H2O molecular? The hydrogen bond may be the
following form:
-N-HO-HO=C-
Dechang Li wrote:
Dear all,
I have two moleculars in the .trr. I want to use g_hbond to analyze the
hydrogen bonds between them. Can g_hbond analyze the hydrogen bonds between
two moleculars associated by a H2O molecular? The hydrogen bond may be the
following form:
Hi all,
Does periodic boundary affect the calculation of hydrogen bond if my
protein is not in one box? What about other calculations?
Thank you,
Tang jiaowei
___
gmx-users mailing listgmx-users@gromacs.org
Hi Tang Jiaowei,
g_hbond takes periodicity into account, like most tools do. Do note
that this doesn't work if you've performed rotational transformations
(lsq-fitting).
Cheers,
Tsjerk
On 9/28/07, tangxuan [EMAIL PROTECTED] wrote:
Hi all,
Does periodic boundary affect the calculation of
Dear all,
I would like to know the actual cut-off angle used by gromacs package to
calculate Hydrogen bond.
since in User manual of version 3.2 and earlier, it was written
á equal to or lesser than áHB = 60 degree
While in User manual of version 3.3, it is mentioned as
á equal to or lesser
Anil Kumar wrote:
Dear all,
I would like to know the actual cut-off angle used by gromacs package to
calculate Hydrogen bond.
since in User manual of version 3.2 and earlier, it was written
á equal to or lesser than áHB = 60 degree
While in User manual of version 3.3, it is mentioned as
á
Hi,
I have some questions about g_hbond option.
1) My system consists of a protein molecule (a capped 1 alanine residue)
(CH3-CO-ALA-NH-CH3) and 250 water molecules. After selecting the g_hbond
option, it says that protein molecule consists of 12 elements; however, it
consists much more
20 dec 2006 kl. 17.34 skrev OZGE ENGIN:
Hi,
I have some questions about g_hbond option.
1) My system consists of a protein molecule (a capped 1 alanine
residue) (CH3-CO-ALA-NH-CH3) and 250 water molecules. After
selecting the g_hbond option, it says that protein molecule
consists of 12
the analysis into parts: solvent-solute ...
/Erik
Thanks in advance
Ozge
-Original Message-
From: Erik Marklund [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Mon, 18 Dec 2006 13:48:18 +0100
Subject: Re: [gmx-users] g_hbond
On Mon, 2006-12
Hi,
I have a problem with g_hbond. I want to investigate the H bonds formed not
only within the protein but also between water molecules and the protein.In
this respect, I select the group 0 -- 'system' option for both selections, an
error message like the following one appears:
Segmentation
On Mon, 2006-12-18 at 13:34 +0200, OZGE ENGIN wrote:
Hi,
I have a problem with g_hbond. I want to investigate the H bonds formed not
only within the protein but also between water molecules and the protein.In
this respect, I select the group 0 -- 'system' option for both selections,
an
Maybe not enough memory. Try using -shell .
On 12/18/06, Erik Marklund [EMAIL PROTECTED] wrote:
On Mon, 2006-12-18 at 13:34 +0200, OZGE ENGIN wrote:
Hi,
I have a problem with g_hbond. I want to investigate the H bonds formed not only
within the protein but also between water molecules and
hi,
On Monday 18 December 2006 12:34, OZGE ENGIN wrote:
Hi,
I have a problem with g_hbond. I want to investigate the H bonds formed not
only within the protein but also between water molecules and the protein.In
this respect, I select the group 0 -- 'system' option for both
selections, an
Message-
From: Erik Marklund [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Mon, 18 Dec 2006 13:48:18 +0100
Subject: Re: [gmx-users] g_hbond
On Mon, 2006-12-18 at 13:34 +0200, OZGE ENGIN wrote:
Hi,
I have a problem with g_hbond. I want to investigate
Besides used for h-bond, g_hbond can be used for determine whether the
distance has fallen into a range (with -nocontact and -r and -r2).
g_dist is not good for calculate for distance between two atoms but
g_mindist can perform this job well. Actually, because of a compulsive
input of tpr
carotti [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Sent: Wednesday, November 22, 2006 10:46 AM
Subject: [gmx-users] g_hbond -contact option
Hi all,
I have found this interesting option in g_hbond, and I would like to
know something more about it. How does it work? Which is the difference
Hi all,
I'm beginning to analyze my trajectories, everything works fine with
(g_rmsf, g_saltbr ...) but when i try to use g_hbond I receive this
error:
--
Program g_hbond, VERSION 3.3.1
Source code file: gmx_hbond.c, line: 631
Fatal error:
Your computational box has shrunk too much.
hello,
after using g_hbond to generate an *.xpm file one sees in the *.xpm file the
following: y-label: Hydrogen Bond Index and the y-axis ranges between 0 and
163. if i look in the additionally generated hbbond.ndx file, i see at the
bottom of it the group [ hbonds_* ]. i assumed that the
[EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wednesday, October 11, 2006 8:21 AM
Subject: [gmx-users] g_hbond
hello,
after using g_hbond to generate an *.xpm file one sees in the *.xpm file the
following: y-label: Hydrogen Bond Index and the y-axis ranges
Ok. I'm on it. A few things I can see right away, other things need a
closer look. See comments below
On Tue, 2006-08-22 at 16:02 -0500, Moore, Jonathan (J) wrote:
I'm still having problems with g_hbond. I've submitted a bugzilla report.
- The hbond existence matrix in the -hbm output does
23, 2006 7:28 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_hbond
Ok. I'm on it. A few things I can see right away, other things need a closer
look. See comments below
On Tue, 2006-08-22 at 16:02 -0500, Moore, Jonathan (J) wrote:
I'm still having problems with g_hbond
I'm still having problems with g_hbond. I've submitted a bugzilla report.
- The hbond existence matrix in the -hbm output does not match the list of
hbonds in the ndx file from -hbn.
- Also, it outputs No option -g when no -g command line option has been
tried
- Also, sometimes the number of
It was a hard nut to crack, but I think I've done it after some sifting
the source code:
Since the -merge option is switched on by default, the hydrogen indexes
are more or less irrelevant for some parts of the code. What happens
here is that g_hbond finds the hbond [10 12 22] (distance: 0.2971
Dear David,
ok. Now I understand HDA criterion. Can you give me a reference
where I can find the differences between HDA criteria and OHD criteria
and why one of them is preferable than the other?
vmd certainly uses the later criteria. Changing the angle criteria
there 44 degrees in vmd picks
Hi,
I am having trouble understanding the criteria for hydrogen bond and
how it is implemented in g_hbond. Defining hydrogen bond for O1--H..O2
by requiring distance(O1, O2) 0.35 nm and angle(O1-H, H-O2) 30
degrees, my own code consistently give lower number of hydrogen bonds
than g_hbond. But
Chinmay Das wrote:
Hi,
I am having trouble understanding the criteria for hydrogen bond and
how it is implemented in g_hbond. Defining hydrogen bond for O1--H..O2
by requiring distance(O1, O2) 0.35 nm and angle(O1-H, H-O2) 30
angle is defined as H-D-A in g_hbond. is that what you mean?
Dear David,
Partly yes, I am not following H-D-A angle trying to visualize two
water molecules
I hope the mail program will not try to format the ascii cartoon below:
H1--O1
\ /H3
H2 O2
\ H4
Which is the angle I should consider? Luzer-Chandler
I have shown hydrogen bond formation between guanidino
side chain of
Arginine and carboxylate in sidechain of Aspartate out
my simulation
result using g_hbond. Now I see those two residues are
well exposed in
solvent. Since g_hbond compute hydrogen bonds based on
only distance and
angles,
Hi XAvier,
Thanks again, I meant the resistance caused due to dielectric of water
separating two charged residues. I doubt whether it will allow the
transfer of charge between them in order for hydrogen bond to be
effected.
With regards,
B.Nataraj
On Thu, 03 Aug 2006 09:25:07 +0200, X.Periole
raja wrote:
Hi XAvier,
Thanks again, I meant the resistance caused due to dielectric of water
separating two charged residues. I doubt whether it will allow the
transfer of charge between them in order for hydrogen bond to be
effected.
It's still unclear.
The hydrogen bonds you find are there
Thanks spoel,
The g_hbond merely report formation of hydrogen bonds because of two
electronegative atoms come closure to certain distance and angle. The
force field used to simulate is also not capable of modeling hydrogen
bond (Afraid whether I am right). If the h_bond computes the hydrogen
bonds
raja wrote:
Thanks spoel,
The g_hbond merely report formation of hydrogen bonds because of two
electronegative atoms come closure to certain distance and angle. The
force field used to simulate is also not capable of modeling hydrogen
bond (Afraid whether I am right). If the h_bond computes the
Dear Spoel,
Thank for your elaborate answer and references. Some times this forum
serves more than just for gromacs, yes it helps to understand some
basics understanding of physical chemistry. I learned lot of fundamental
concepts of protein modeling in this forum, which I could never
understand
Hi all,
I have shown hydrogen bond formation between guanidino side chain of
Arginine and carboxylate in sidechain of Aspartate out my simulation
result using g_hbond. Now I see those two residues are well exposed in
solvent. Since g_hbond compute hydrogen bonds based on only distance and
angles,
Hi list,
I couldn't find in the archives and 3.2 to 3.3 changes what happened
to -g flag in g_hbond ?
Is the old hbond.log information written somewhere else ?
Diego Enry.
// command line
g_hbond_331i -g(intel compiled)
// error message:
Program g_hbond_331i, VERSION 3.3.1
Source code
Upgraded it to 3.3.1 now, still get the same error ...
Using this command:
g_hbond -f ../76.55-78.95ns.xtc -s ../md_000.tpr -n index.ndx -num
hbnum_MGL-MGL
I get this output:
Reading file ../md_000.tpr,
Michael Torrice wrote:
I am confused about the output from the hblife.xvg file of g_hbond.
What exactly is the p(t) output? Is it the percent distribution of a
given lifetime? If so, I have received p(t) data that sums up to
anything from 0.1 toi 2.
Check my recent paper:
David van der
-users] g_hbond question
hi jonathan,
the actually occuring hydrogen bonds are listed in the log-file.
daniela
On Tue, 2006-03-21 at 14:56 -0800, Moore, Jonathan (J) wrote:
I created a hydrogen bond map using g_hbond of version 3.3. The
manual indicates that for the hbmap the Ordering
I created a hydrogen bond map using g_hbond of version 3.3. The manual
indicates that for the hbmap the Ordering is identical to that in -hbn index
file. However, in my case, the hbmap file contains 13 hydrogen bond indices,
but the hbond.ndx file lists 20 sets of donors and acceptors. Why
hi jonathan,
the actually occuring hydrogen bonds are listed in the log-file.
daniela
On Tue, 2006-03-21 at 14:56 -0800, Moore, Jonathan (J) wrote:
I created a hydrogen bond map using g_hbond of version 3.3. The manual
indicates that for the hbmap the Ordering is identical to that in
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