subject:"\[gmx\-users\] g

Dear users,

I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was compared with another simulation.
It was found that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.
The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.

Why is this difference in index and xvg output?
Also the xvg file looks like -

s0 legend Contacts
@ s1 legend Pairs within 0.4 nm
  40007496   0
  40027513   0
  40047605   0
  40067531   0
  40087573   0
  40107546   0
  40127544   0
  40147526   0
  40167530   0
  40187496   0
  40207526   0
..


Thank you
kavya
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Re: [gmx-users] g_hbond and contact

2013-03-04 Thread Justin Lemkul




On 3/4/13 11:25 AM, Kavyashree M wrote:

Dear users,

I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg

From the index file, the number of contacts of each atom was extracted.

This and the
xvg output was compared with another simulation.
It was found that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.


These statements don't make any sense.  How did you determine that the number of 
contacts in simulation 2 was greater than simulation 1, but then the .xvg files 
showed the opposite?  The number of contacts come from the .xvg files?  Perhaps 
you simply swapped your files during analysis.



The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.

Why is this difference in index and xvg output?


An index group is a list of atom numbers.  The .xvg output is whatever you tell 
it to be, in this case, the number of contacts within the group selected.


-Justin


Also the xvg file looks like -

s0 legend Contacts
@ s1 legend Pairs within 0.4 nm
   40007496   0
   40027513   0
   40047605   0
   40067531   0
   40087573   0
   40107546   0
   40127544   0
   40147526   0
   40167530   0
   40187496   0
   40207526   0
..


Thank you
kavya



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_hbond and contact

Sir,

From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
[ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]

second section : the unique contacts of each atoms with others
[ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
5 7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5292
5296
530

From this second section Total contacts was extracted for each atom and
compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 Total/mean
@ legend string 1 Total
@ legend string 2 Mean
@ legend string 3 # atoms
@ legend string 4 Mean/# atoms
#resratio tot mean natm mean/atm
1 1.001 1110.991110.991
2 1.244 10 8.0411 8.041
3 1.166 1311.147111.147
4 1.036 1110.615110.615

While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..

I hope I am clear this time.

Thank you
kavya

On Mon, Mar 4, 2013 at 10:05 PM, Justin Lemkul jalem...@vt.edu wrote:

On 3/4/13 11:25 AM, Kavyashree M wrote:

Dear users,

I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn
a.ndx
-num a.xvg

From the index file, the number of contacts of each atom was extracted.

This and the
xvg output was compared with another simulation.
It was found that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.

These statements don't make any sense. How did you determine that the
number of contacts in simulation 2 was greater than simulation 1, but then
the .xvg files showed the opposite? The number of contacts come from the
.xvg files? Perhaps you simply swapped your files during analysis.

The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.

Why is this difference in index and xvg output?

An index group is a list of atom numbers. The .xvg output is whatever you
tell it to be, in this case, the number of contacts within the group
selected.

-Justin

Also the xvg file looks like -

s0 legend Contacts
@ s1 legend Pairs within 0.4 nm
40007496 0
40027513 0
40047605 0
40067531 0
40087573 0
40107546 0
40127544 0
40147526 0
40167530 0
40187496 0
40207526 0
..

Thank you
kavya

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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Re: [gmx-users] g_hbond and contact

2013-03-04 Thread Justin Lemkul




On 3/4/13 12:04 PM, Kavyashree M wrote:

Sir,


From Index file which gives the unique contacts -

First section the list of atoms I want to analyse


When measuring contacts, you don't measure one group, you measure the number of 
contacts that occur between groups A and B, which considers all atoms in those 
two groups.



[ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]

second section : the unique contacts of each atoms with others


You don't define contacts in an index group, you define atoms that may or may 
not make contacts with others.



[ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
   5  7ws
   5 10
   5 14
   5 18
   5 22
   5 24
   5 27
   5 30
   5 35
   5292
   5296
   530



There's something very wrong with this index file.  How did you generate it? 
The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me 
to believe that you've done something incorrect.  Did this come from g_hbond? 
It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, 
nothing else.



From this second section Total contacts was extracted for each atom and

compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 Total/mean
@ legend string 1 Total
@ legend string 2 Mean
@ legend string 3 # atoms
@ legend string 4 Mean/# atoms
#resratio  tot  mean  natm  mean/atm
   1 1.001   1110.991110.991
   2 1.244   10 8.0411 8.041
   3 1.166   1311.147111.147
   4 1.036   1110.615110.615


While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..



That shouldn't be unexpected.  Two independent simulations have no guarantee of 
doing the same thing, that's why sampling is so important.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] g_hbond and contact

On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:


 When measuring contacts, you don't measure one group, you measure the
 number of contacts that occur between groups A and B, which considers all
 atoms in those two groups.


I gave a group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46  -fx.xtc-s   x.tpr-contact   -n   x.ndx   -r   0.4
-hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
my index file contained a group of hydrophobic atoms. which I supplied in
the x.ndx.



  You don't define contacts in an index group, you define atoms that may or
 may not make contacts with others.


The one I mentioned here is the output index file from the g_hbond (4.6
version) - o.ndx.



  [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2
 ]
5  7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5292
5296
530


 There's something very wrong with this index file.  How did you generate
 it? The presence of a repeated atom number (5) and a nonsensical one (7ws)
 leads me to believe that you've done something incorrect.  Did this come
 from g_hbond? It looks like the output of -hbn, which is only useful for
 decoding hbmap.xpm, nothing else.


I did not generate this. The tool (g_hbond) generated this index file. It
is the -hbn output.



  From this second section Total contacts was extracted for each atom and

 compared with
 that from a second simulation.
 These contacts was matching with the contacts of the 3rd column from
 g_mdmat output -
 @ legend string 0 Total/mean
 @ legend string 1 Total
 @ legend string 2 Mean
 @ legend string 3 # atoms
 @ legend string 4 Mean/# atoms
 #resratio  tot  mean  natm  mean/atm
1 1.001   1110.991110.991
2 1.244   10 8.0411 8.041
3 1.166   1311.147111.147
4 1.036   1110.615110.615


 While the time dependent contacts in the xvg file shows that the first
 simulation has more
 contacts than the second one..


 That shouldn't be unexpected.  Two independent simulations have no
 guarantee of doing the same thing, that's why sampling is so important.


Thank you
kavya
-- 
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Re: [gmx-users] g_hbond and contact

2013-03-04 Thread Justin Lemkul




On 3/4/13 1:10 PM, Kavyashree M wrote:

On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:



When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.



I gave a group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46  -fx.xtc-s   x.tpr-contact   -n   x.ndx   -r   0.4
-hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
my index file contained a group of hydrophobic atoms. which I supplied in
the x.ndx.




  You don't define contacts in an index group, you define atoms that may or
may not make contacts with others.



The one I mentioned here is the output index file from the g_hbond (4.6
version) - o.ndx.




  [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2

]
5  7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5292
5296
530



There's something very wrong with this index file.  How did you generate
it? The presence of a repeated atom number (5) and a nonsensical one (7ws)
leads me to believe that you've done something incorrect.  Did this come
from g_hbond? It looks like the output of -hbn, which is only useful for
decoding hbmap.xpm, nothing else.



I did not generate this. The tool (g_hbond) generated this index file. It
is the -hbn output.




OK, then I still don't know what 7ws is, but the only purpose for this file is 
to provide a key to the existence matrix in hbmap.xpm.  Your previous 
description indicated that you were using it for some other analysis, which 
would not be appropriate.


The other thing worth mentioning here is something that was posted to the list 
just a few hours ago, that the output of g_hbond -contact may not agree with 
other methods of calculating contacts, especially in the case of -merge vs. 
-nomerge.


-Justin



  From this second section Total contacts was extracted for each atom and



compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 Total/mean
@ legend string 1 Total
@ legend string 2 Mean
@ legend string 3 # atoms
@ legend string 4 Mean/# atoms
#resratio  tot  mean  natm  mean/atm
1 1.001   1110.991110.991
2 1.244   10 8.0411 8.041
3 1.166   1311.147111.147
4 1.036   1110.615110.615


While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..



That shouldn't be unexpected.  Two independent simulations have no
guarantee of doing the same thing, that's why sampling is so important.



Thank you
kavya



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] g_hbond and contact

I am sorry There is no 7ws Its a typographic error. What I wanted to ask
was -
I am comparing two simulations S1 and S2 for contacts at a given cut off
I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of -num and -hbn was considered.
1. -hbn output was analysed to calculate how many contacts each
atom has from both S1 and S2.
2. -num output graph was compared from both S1 and S2.
g_mdmat output: of -no was considered.
3. -no output was analysed from both S1 and S2 using the
third column or the second Y value which gives total
contacts
of each atom.

It was observed that 1 and 3 matched exactly giving the same number of
contacts each atom has (in the whole simulations). indicating that the
number
of contacts each atom has was more in S2 than S1.

But the graph from 2 indicated that the number of contacts (along the
trajectory)
in S1 was higher than S2.

My doubt is:
The number of contact per atom follows S2 S1
while number of contacts per time follows S1 S2.
I am unclear as to what I have to conclude from this observations.

- I used the same cutoff throughout.
- There has not been any swapping of the trajectory while analysing.

Thank you
Kavya

On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul jalem...@vt.edu wrote:

On 3/4/13 1:10 PM, Kavyashree M wrote:

On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:

When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.

I gave a group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4
-hbm o.xpm -hbn o.ndx -num o.xvg
my index file contained a group of hydrophobic atoms. which I supplied in
the x.ndx.

You don't define contacts in an index group, you define atoms that may
or
may not make contacts with others.

The one I mentioned here is the output index file from the g_hbond (4.6
version) - o.ndx.

[ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_***
*CZ2_CZ3_CH2

]
5 7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5292
5296
530

There's something very wrong with this index file. How did you
generate
it? The presence of a repeated atom number (5) and a nonsensical one
(7ws)
leads me to believe that you've done something incorrect. Did this come
from g_hbond? It looks like the output of -hbn, which is only useful for
decoding hbmap.xpm, nothing else.

I did not generate this. The tool (g_hbond) generated this index file.
It
is the -hbn output.

OK, then I still don't know what 7ws is, but the only purpose for this
file is to provide a key to the existence matrix in hbmap.xpm. Your
previous description indicated that you were using it for some other
analysis, which would not be appropriate.

The other thing worth mentioning here is something that was posted to the
list just a few hours ago, that the output of g_hbond -contact may not
agree with other methods of calculating contacts, especially in the case of
-merge vs. -nomerge.

-Justin

From this second section Total contacts was extracted for each atom and

compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 Total/mean
@ legend string 1 Total
@ legend string 2 Mean
@ legend string 3 # atoms
@ legend string 4 Mean/# atoms
#resratio tot mean natm mean/atm
1 1.001 1110.991110.991
2 1.244 10 8.0411 8.041
3 1.166 1311.147111.147
4 1.036 1110.615110.615

While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..

That shouldn't be unexpected. Two independent simulations have no
guarantee of doing the same thing, that's why sampling is so important.

Thank you
kavya

--
==**==

[gmx-users] g_hbond existence matrix

2013-01-24 Thread Kavyashree M

Dear users,

I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
   c #FF  /* None */,
o  c #FF  /* Present */,
Meaning -
character space in white colour means Hbond not present
character o in red colour means Hbond is present.

In addition, the file also contains white coloured o what is
this?

Thank you
Kavya
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Re: [gmx-users] g_hbond existence matrix

2013-01-24 Thread Justin Lemkul




On 1/24/13 11:03 AM, Kavyashree M wrote:

Dear users,

I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
   c #FF  /* None */,
o  c #FF  /* Present */,
Meaning -
character space in white colour means Hbond not present
character o in red colour means Hbond is present.

In addition, the file also contains white coloured o what is
this?



There are only two characters in the .xpm file, a space and an 'o' as you noted 
above.  The font color that appears in your terminal is whatever you have set it 
to be; there is no significance of different colored letters in the .xpm file. 
There either is a hydrogen bond in a frame (in which case you see 'o') or there 
is not (and thus a blank space).


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] g_hbond existence matrix

2013-01-24 Thread Kavyashree M

Thank you for the clarification.

On Fri, Jan 25, 2013 at 12:40 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 1/24/13 11:03 AM, Kavyashree M wrote:

 Dear users,

 I have a little confusion -
 The hbmap.xpm file gives the existence of each hydrogen bond.
 The file mentions -
c #FF  /* None */,
 o  c #FF  /* Present */,
 Meaning -
 character space in white colour means Hbond not present
 character o in red colour means Hbond is present.

 In addition, the file also contains white coloured o what is
 this?


 There are only two characters in the .xpm file, a space and an 'o' as you
 noted above.  The font color that appears in your terminal is whatever you
 have set it to be; there is no significance of different colored letters in
 the .xpm file. There either is a hydrogen bond in a frame (in which case
 you see 'o') or there is not (and thus a blank space).

 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
 --
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 Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
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Re: [gmx-users] g_hbond index

2012-12-19 Thread Justin Lemkul




On 12/19/12 9:37 AM, Kavyashree M wrote:

Dear users,

While using g_hbond, does it make any difference if I give option
18 and 1 or 1 and 18?


Order does not matter.


I wanted to find the hydrogen bonding of a group of residues with
the whole protein so I had an index of this group. When I give the
option as 18 (index number) and 1 (whole protein), I get several
messages
Hm. This isn't the first time I found this donor (...,...)
But later it does calculates. does this mean that it is double counting
those interactions?



What is group 18?  Be mindful of the g_hbond requirement that the chosen groups 
must be completely unique or completely overlapping.


-Justin

--


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Department of Biochemistry
Virginia Tech
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Re: [gmx-users] g_hbond index

2012-12-19 Thread Kavyashree M

Sir,

I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.

Group 18 is a set of residues in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the whole
protein. so group 18 is a subset of group 1.


Thank you
Kavya
On Wed, Dec 19, 2012 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 12/19/12 9:37 AM, Kavyashree M wrote:

 Dear users,

 While using g_hbond, does it make any difference if I give option
 18 and 1 or 1 and 18?


 Order does not matter.


  I wanted to find the hydrogen bonding of a group of residues with
 the whole protein so I had an index of this group. When I give the
 option as 18 (index number) and 1 (whole protein), I get several
 messages
 Hm. This isn't the first time I found this donor (...,...)
 But later it does calculates. does this mean that it is double counting
 those interactions?


 What is group 18?  Be mindful of the g_hbond requirement that the chosen
 groups must be completely unique or completely overlapping.

 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] g_hbond index

2012-12-19 Thread Justin Lemkul




On 12/19/12 11:43 AM, Kavyashree M wrote:

Sir,

I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.

Group 18 is a set of residues in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the whole
protein. so group 18 is a subset of group 1.



You see a difference likely because you are invoking the command incorrectly 
(with overlapping index groups) and it is affecting the way the donor and 
acceptor arrays are constructed.  The proper method of analysis is to monitor 
H-bonds within group 18 and then between group 18 and whatever part of the 
protein that does not overlap with it.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] g_hbond index

2012-12-19 Thread Kavyashree M

Ok thank you.

kavya

On Wed, Dec 19, 2012 at 10:52 PM, Justin Lemkul jalem...@vt.edu wrote:

On 12/19/12 11:43 AM, Kavyashree M wrote:

Sir,

I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.

Group 18 is a set of residues in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the whole
protein. so group 18 is a subset of group 1.

You see a difference likely because you are invoking the command
incorrectly (with overlapping index groups) and it is affecting the way the
donor and acceptor arrays are constructed. The proper method of analysis
is to monitor H-bonds within group 18 and then between group 18 and
whatever part of the protein that does not overlap with it.

-Justin

--
==**==

[gmx-users] g_hbond routine

2012-11-30 Thread Velia Minicozzi


Dear gromacs users,

in the Gromacs manual pages (version 4.5.3 page 211) there are the 
criteria to have an Hbond.

r  0.35 nm, where r is the Donor-Acceptor distance
alpha  30°, where alpha is the Hydrogen-Donor-Acceptor angle

in the Manual page for g_hbond (version 4.5.3 page 275) it is written
Hydrogen bonds are determined based on cutoffs for the
angle Acceptor - Donor - Hydrogen (zero is extended) and the distance 
Hydrogen - Acceptor


and even in the file that exits by using the option -dist the xaxis 
label is Hydrogen - Acceptor Distance (nm)
but I think this is the Donor-Acceptor distance because it seems too big 
to be the Hydrogen-Acceptor distance.

Which distance is it?

Thank you very much,

Velia


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Re: [gmx-users] g_hbond routine

2012-11-30 Thread Justin Lemkul




On 11/30/12 10:41 AM, Velia Minicozzi wrote:

Dear gromacs users,

in the Gromacs manual pages (version 4.5.3 page 211) there are the criteria to
have an Hbond.
r  0.35 nm, where r is the Donor-Acceptor distance
alpha  30°, where alpha is the Hydrogen-Donor-Acceptor angle

in the Manual page for g_hbond (version 4.5.3 page 275) it is written
Hydrogen bonds are determined based on cutoffs for the
angle Acceptor - Donor - Hydrogen (zero is extended) and the distance Hydrogen -
Acceptor

and even in the file that exits by using the option -dist the xaxis label is
Hydrogen - Acceptor Distance (nm)
but I think this is the Donor-Acceptor distance because it seems too big to be
the Hydrogen-Acceptor distance.
Which distance is it?



It depends on what you select.  You control whether it is the H-A or D-A 
distance using the -da flag.  By default, it is a D-A distance.  There is small 
output bug was reported this morning and there is an open Redmine issue for it. 
 It is low-priority, but will be fixed sometime in the future.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_hbond

2012-09-28 Thread Gavin Melaugh

Hi

I have an alcohol system and I want to calculate the number of H bonds
during the trajectory.
My atom type labels are C2-C2-C2-CO-OH-HO.  CO denotes carbon bonded to
oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen.
In g_hbond how do I specify my groups to consider for H bonding. If I
uses group 0 which is the whole system it says that I have twice as many
acceptors as donors, which shouldn't be the case.

Cheers

Gavin
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Re: [gmx-users] g_hbond

2012-09-28 Thread Justin Lemkul




On 9/28/12 8:53 AM, Gavin Melaugh wrote:

Hi

I have an alcohol system and I want to calculate the number of H bonds
during the trajectory.
My atom type labels are C2-C2-C2-CO-OH-HO.  CO denotes carbon bonded to
oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen.
In g_hbond how do I specify my groups to consider for H bonding. If I
uses group 0 which is the whole system it says that I have twice as many
acceptors as donors, which shouldn't be the case.



g_hbond uses atom names (not types) to determine what is considered a donor, 
acceptor, or H atom.  If there is a problem with the number of acceptors or 
donors, then there is a problem with the way the atoms are named.  Without 
seeing the [atoms] section of the topology or relevant snippet of the coordinate 
file, it's hard to say what's going on at this point.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_hbond

2012-04-05 Thread Nilesh Dhumal

Hello,

How can I add chlorin atom as a acceptor in g_hbond.

I am using  Gromacs VERSION 4.0.7

NIlesh




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Re: [gmx-users] g_hbond

2012-04-05 Thread Justin A. Lemkul




Nilesh Dhumal wrote:

Hello,

How can I add chlorin atom as a acceptor in g_hbond.



Either modify the source code (the search_acceptors routine in gmx_hbond.c) or 
make a dummy structure/topology that lists the Cl atoms as O.  The program 
searches for acceptors by atom name only (O and/or N if using -nitacc), so you 
can probably trick it into thinking that's what they are.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] g_hbond

2011-12-20 Thread sulatha M. S

As suggested by David I extended the simulations (total of 25ns) for a
single chain polyacid in 5500 water molecules and tried to calculate the
H-bond ACF. I get the same negative lifetime for Hbonds between COOH groups
and water. Is it that the g_hbond ACF giving weird results for this case.
For chains with COO- and COOH groups (50% each), I got positive life times
of Hbond. Ayy ideas on how to solve this will be of great help. I am using
4.0.7 version. The command line I gave was
g_hbond -f traj.xtc -s traj.tpr -n index.ndx -ac and chose the polyacid and
the water as  the two groups.


ACF 22057/22057
Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 =  0.0146697
Q =  0
--

Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward-0.271 -3.687-666.000   0.0146697
Backward   -2.291 -0.437-666.000
One-way 0.101  9.882  10.207
Integral0.034 29.376  12.907
Relaxation  0.063 15.803  11.370


Thankyou for any help,

Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India


On Tue, Dec 13, 2011 at 10:12 AM, sulatha M. S mssula...@gmail.com wrote:



 I did not get a warning here. I also have simulations (20ns) of
 copolyacids where again it gave me negative life time. These runs are
 well equilibrated with respect to energy and Rg of the polymers. The
 system is a 20 repeat unit chain in approx. 5500 water molecules. I have
 done simulations in which 10 units are COO- and the remaining 10 as COOH
 along the chain. With a 10ns trajectory, the average life time of
 H-bonds is positive.Only in the case of unionized acid I am getting a
 negative life time.

  Did you look at the ACF graph? It could be constant at 1 or 0.


 Yes, the ACF decays to 0 and remains constant in all cases





Thankyou for any help,

Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] g_hbond

2011-12-12 Thread sulatha M. S

Dear David,

Yes it is DGact.
 The DGeq follows from the fraction of COOH that are not forming hydrogen
 bonds, option -nhbdist.


So, I need to use the equation (9) and (10) from your paper to calculate
the equilibrium constant and free energy of H-bonding.


 Another question I have is, for a polycarboxylic acid system in water
 (COOH groups as side chains) for a 10ns run, I got the following as the
 output where the life time of the H-bond (between the polyacid and
 water) is negative. Is this correct?

 This means that the ACF has not equilibrated and you need much longer
 sims. You probably got a warning about it.


I did not get a warning here. I also have simulations (20ns) of copolyacids
where again it gave me negative life time. These runs are well equilibrated
with respect to energy and Rg of the polymers. The system is a 20 repeat
unit chain in approx. 5500 water molecules. I have done simulations in
which 10 units are COO- and the remaining 10 as COOH along the chain. With
a 10ns trajectory, the average life time of H-bonds is positive.Only in the
case of unionized acid I am getting a negative life time.


 ACF 22057/22057
 Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
 Hydrogen bond thermodynamics at T = 298.15 K
 Fitting parameters chi^2 =  0.0146697
 Q =  0
 --
 Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
 Forward-0.271 -3.687-666.000   0.0146697
 Backward   -2.291 -0.437-666.000
 One-way 0.101  9.882  10.207
 Integral0.034 29.376  12.907
 Relaxation  0.063 15.803  11.370


 Thankyou for any help,

 Dr. M. S. Sulatha
 Dept. of Chemical Engineering
 IIT-Madras
 India




-- 
 David van der Spoel, Ph.D., Professor of Biology
 Dept. of Cell  Molec. Biol., Uppsala University.
 Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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What is the value for free energy of H-bonding.

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Re: [gmx-users] g_hbond

2011-12-12 Thread David van der Spoel


On 2011-12-12 09:54, sulatha M. S wrote:

Dear David,

Yes it is DGact.
The DGeq follows from the fraction of COOH that are not forming
hydrogen bonds, option -nhbdist.


So, I need to use the equation (9) and (10) from your paper to calculate
the equilibrium constant and free energy of H-bonding.

Yes.




Another question I have is, for a polycarboxylic acid system in
water
(COOH groups as side chains) for a 10ns run, I got the following
as the
output where the life time of the H-bond (between the polyacid and
water) is negative. Is this correct?

This means that the ACF has not equilibrated and you need much
longer sims. You probably got a warning about it.


I did not get a warning here. I also have simulations (20ns) of
copolyacids where again it gave me negative life time. These runs are
well equilibrated with respect to energy and Rg of the polymers. The
system is a 20 repeat unit chain in approx. 5500 water molecules. I have
done simulations in which 10 units are COO- and the remaining 10 as COOH
along the chain. With a 10ns trajectory, the average life time of
H-bonds is positive.Only in the case of unionized acid I am getting a
negative life time.


Did you look at the ACF graph? It could be constant at 1 or 0.


ACF 22057/22057
Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 =  0.0146697
Q =  0
--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward-0.271 -3.687-666.000   0.0146697
Backward   -2.291 -0.437-666.000
One-way 0.101  9.882  10.207
Integral0.034 29.376  12.907
Relaxation  0.063 15.803  11.370


Thankyou for any help,

Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se
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What is the value for free energy of H-bonding.







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Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] g_hbond

2011-12-12 Thread sulatha M. S

I did not get a warning here. I also have simulations (20ns) of
 copolyacids where again it gave me negative life time. These runs are
 well equilibrated with respect to energy and Rg of the polymers. The
 system is a 20 repeat unit chain in approx. 5500 water molecules. I have
 done simulations in which 10 units are COO- and the remaining 10 as COOH
 along the chain. With a 10ns trajectory, the average life time of
 H-bonds is positive.Only in the case of unionized acid I am getting a
 negative life time.

  Did you look at the ACF graph? It could be constant at 1 or 0.


Yes, the ACF decays to 0 and remains constant in all cases





Thankyou for any help,

Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se

http://folding.bmc.uu.se
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[gmx-users] g_hbond

2011-12-11 Thread sulatha M. S

Dear gromacs users,

I did a g_hbond -ac analysis on a 10 ns trajectory of a polycarboxylate in
water. Following is the output I obtained for the polycarboxylate H-bondign
with water

ACF 36008/36008
Normalization for c(t) = 0.00709164 for gh(t) = 7.09124e-07
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 0.000661899
Q =  0
--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 0.300  3.334   7.513  0.000661899
Backward1.608  0.622   3.350
One-way 0.089 11.284  10.536
Integral0.039 25.374  12.544
Relaxation  0.062 16.080  11.413

I have read David paper (2006) on thermodynamics of H-bonding. In the paper
two delta G values are mentioned. one is the Gibbs energy of activation
(dG#) and another is the free energy of H-bonding. In the output given from
the -ac analysis, which dG values do these correspond to? I assumed dG
given for the forward rate correspond to the energy of activation. Is it
correct? What is the value for free energy of H-bonding.

Another question I have is, for a polycarboxylic acid system in water (COOH
groups as side chains) for a 10ns run, I got the following as the output
where the life time of the H-bond (between the polyacid and water) is
negative. Is this correct?

ACF 22057/22057
Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 =  0.0146697
Q =  0
--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward-0.271 -3.687-666.000   0.0146697
Backward   -2.291 -0.437-666.000
One-way 0.101  9.882  10.207
Integral0.034 29.376  12.907
Relaxation  0.063 15.803  11.370


Thankyou for any help,

Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India
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Re: [gmx-users] g_hbond

2011-12-11 Thread David van der Spoel


On 2011-12-12 07:41, sulatha M. S wrote:

Dear gromacs users,

I did a g_hbond -ac analysis on a 10 ns trajectory of a polycarboxylate
in water. Following is the output I obtained for the polycarboxylate
H-bondign with water

ACF 36008/36008
Normalization for c(t) = 0.00709164 for gh(t) = 7.09124e-07
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 0.000661899
Q =  0
--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 0.300  3.334   7.513  0.000661899
Backward1.608  0.622   3.350
One-way 0.089 11.284  10.536
Integral0.039 25.374  12.544
Relaxation  0.062 16.080  11.413

I have read David paper (2006) on thermodynamics of H-bonding. In the
paper two delta G values are mentioned. one is the Gibbs energy of
activation (dG#) and another is the free energy of H-bonding. In the
output given from the -ac analysis, which dG values do these correspond
to? I assumed dG given for the forward rate correspond to the energy of
activation. Is it correct? What is the value for free energy of H-bonding.

Yes it is DGact.
The DGeq follows from the fraction of COOH that are not forming hydrogen 
bonds, option -nhbdist.




Another question I have is, for a polycarboxylic acid system in water
(COOH groups as side chains) for a 10ns run, I got the following as the
output where the life time of the H-bond (between the polyacid and
water) is negative. Is this correct?
This means that the ACF has not equilibrated and you need much longer 
sims. You probably got a warning about it.




ACF 22057/22057
Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 =  0.0146697
Q =  0
--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward-0.271 -3.687-666.000   0.0146697
Backward   -2.291 -0.437-666.000
One-way 0.101  9.882  10.207
Integral0.034 29.376  12.907
Relaxation  0.063 15.803  11.370


Thankyou for any help,

Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India





--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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[gmx-users] g_hbond -hbn

2011-11-07 Thread Yao Yao

Hi Gmxers,

I used g_hbond -n protein.ndx -hbn output.xvg 

to get the index of all the atoms forming H-bond with the protein, 

but since H-Bonds should be dynamic as time evolves, I should see changing 
number of HBonds in the output.xvg which I have not seen yet.
Kinda confused.

Thanks,

Yao  
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Re: [gmx-users] g_hbond -hbn

2011-11-07 Thread Justin A. Lemkul




Yao Yao wrote:

Hi Gmxers,

I used g_hbond -n protein.ndx -hbn output.xvg
to get the index of all the atoms forming H-bond with the protein,
but since H-Bonds should be dynamic as time evolves, I should see 
changing number of HBonds in the output.xvg which I have not seen yet.

Kinda confused.



The output of -hbn is an index file, not an .xvg file.  The index file can be 
mapped to the output of -hbm, which is an existence matrix of the hydrogen 
bonds.  Some may swap simultaneously, so you may not see dramatic changes in the 
output of -num (the number of hydrogen bonds).


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_hbond frames

2011-10-16 Thread Yao Yao

Hi Gmxers,

I ran g_hbond between my protein and water for a 3ns trajectory with 2 fs 
integration step but found the error,

Cannot calculate autocorrelation of life times with less than two frames,

I am quite sure my system is just a regular protein in a cubic water box. 

And the size of trajectory is big with no error messages when finished.
So it should not be just a couple of frames. 

Anyone met this before?


Thanks,

Yao
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Re: [gmx-users] g_hbond frames

2011-10-16 Thread Justin A. Lemkul




Yao Yao wrote:

Hi Gmxers,

I ran g_hbond between my protein and water for a 3ns trajectory with 2 
fs integration step but found the error,


Cannot calculate autocorrelation of life times with less than two frames,

I am quite sure my system is just a regular protein in a cubic water box.
And the size of trajectory is big with no error messages when finished.
So it should not be just a couple of frames.
Anyone met this before?



Without providing the exact command you used, there's little anyone can do to 
help.  In addition, you may want to run gmxcheck on your trajectory to make sure 
there are no corrupt frames.


-Justin


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_hbond

2011-10-10 Thread Mr Bernard Ramos

Hi everyone!

I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are 
counted/determined by g_hbond based on angle and distance cut-offs. The 
distance cut-off is based on the acceptor-donor distance. However, the online 
manual says that the distance is based on Hydrogen - Acceptor distance? The 
link to the online manual is as follows: 

http://manual.gromacs.org/online/g_hbond.html


I am using Gromacs 4.5.3. I found out that g_hbond does not give the correct 
counts due to a bug

http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html


I am fairly new to using Gromacs with limited knowledge in programming. How do 
I get this bug fixed with my current version? How can I patch the fix suggested 
above?

The other question will be. Does the most recent version has the g_hbond fixed? 
I use Gromacs via Cygwin. Just in case I install the the new version, I would 
like to keep my old one. Is it ok, or do I have remove it?

Thanks.    

Bernard-- 
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[gmx-users] g_hbond

2011-10-10 Thread Mr Bernard Ramos

Hi everyone!

I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are 
counted/determined by g_hbond based on angle and distance cut-offs. The 
distance cut-off is based on the acceptor-donor distance. However, the online 
manual says that the distance is based on Hydrogen - Acceptor distance? The 
link to the online manual is as follows: 

http://manual.gromacs.org/online/g_hbond.html

I am using Gromacs 4.5.3. I found out that g_hbond does not give the correct 
counts due to a bug

http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html

I am fairly new to using Gromacs with limited knowledge in programming. How do 
I get this bug fixed with my current version? How can I patch the fix suggested 
above?

The other question will be. Does the most recent version has the g_hbond fixed? 
I use Gromacs via Cygwin. Just in case I install the the new version, I would 
like to keep my old one. Is it ok, or do I have remove it?

Thanks.    

Bernard-- 
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Re: [gmx-users] g_hbond

2011-10-10 Thread Justin A. Lemkul




Mr Bernard Ramos wrote:

Hi everyone!

I have some questions on g_hbond. According to Manual 4.5.4, 
hydrogen-bonds are counted/determined by g_hbond based on angle and 
distance cut-offs. The distance cut-off is based on the acceptor-donor 
distance. However, the online manual says that the distance is based on 
Hydrogen - Acceptor distance? The link to the online manual is as follows: 


http://manual.gromacs.org/online/g_hbond.html



It should be the donor-acceptor distance.  There was some discussion on this a 
few weeks ago.  The code


I am using Gromacs 4.5.3. I found out that g_hbond does not give the 
correct counts due to a bug


http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html

I am fairly new to using Gromacs with limited knowledge in programming. 
How do I get this bug fixed with my current version? How can I patch the 
fix suggested above?




I wouldn't bother.  That would require cherry-picking a commit from the git 
repository.  Just upgrade to the latest version of Gromacs and it will be fixed.


The other question will be. Does the most recent version has the g_hbond 
fixed? I use Gromacs via Cygwin. Just in case I install the the new 
version, I would like to keep my old one. Is it ok, or do I have remove it?




You can maintain different versions concurrently as long as they are in discrete 
locations and you configure your environment to access the proper one (i.e. by 
sourcing the right GMXRC file).


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_hbond

2011-10-10 Thread Justin A. Lemkul




Justin A. Lemkul wrote:



Mr Bernard Ramos wrote:

Hi everyone!

I have some questions on g_hbond. According to Manual 4.5.4, 
hydrogen-bonds are counted/determined by g_hbond based on angle and 
distance cut-offs. The distance cut-off is based on the acceptor-donor 
distance. However, the online manual says that the distance is based 
on Hydrogen - Acceptor distance? The link to the online manual is as 
follows:

http://manual.gromacs.org/online/g_hbond.html



It should be the donor-acceptor distance.  There was some discussion on 
this a few weeks ago.  The code




Oops, forgot to finish that thought.  Someone came into my office...

Where I was going was that the code is very convoluted and I honestly can't 
follow it, so hopefully a developer can confirm the proper action so the 
documentation can be updated.


-Justin

I am using Gromacs 4.5.3. I found out that g_hbond does not give the 
correct counts due to a bug


http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html

I am fairly new to using Gromacs with limited knowledge in 
programming. How do I get this bug fixed with my current version? How 
can I patch the fix suggested above?




I wouldn't bother.  That would require cherry-picking a commit from the 
git repository.  Just upgrade to the latest version of Gromacs and it 
will be fixed.


The other question will be. Does the most recent version has the 
g_hbond fixed? I use Gromacs via Cygwin. Just in case I install the 
the new version, I would like to keep my old one. Is it ok, or do I 
have remove it?




You can maintain different versions concurrently as long as they are in 
discrete locations and you configure your environment to access the 
proper one (i.e. by sourcing the right GMXRC file).


-Justin



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_hbond

2011-09-01 Thread Steven Neumann

On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Steven Neumann wrote:

 One question for Glycine it is easy to assess 3 possible hbonds which
 can create as hydrogen is only one atom as a side chain.
 How about other amino acids and their maximum hbonds they can create?



 Any OH or NH group is a donor, any lone pair is an acceptor (though
 obviously not modeled explicitly in MD).  The ability of MD force fields to
 agree with reality in this respect is debatable, but should come close.

 -Justin




 Thank you Justin. Can you please clarify me something and tell me whether I
 am wrong. This is what I obtained from calulating hbonds between 10 ligands
 and Glycine. Each ligand serve 8 OH group (flavanoid) :


*Reading file md.tpr, VERSION 4.5.4 (single precision)
Specify 2 groups to analyze:
Group 0 (   r_96) has 7 elements -* this is my Glycine -
7 atoms (side chain - Hydrogen)
*Group 1 (LIG) has   510 elements-* these are 10
ligands, 51 atoms each, 8 OH group
*Select a group: 0 1
Selected 0: 'r_96'
Select a group: Selected 1: 'LIG'
Checking for overlap in atoms between r_96 and LIG
Calculating hydrogen bonds between r_96 (7 atoms) and LIG (510 atoms)
Found 81 donors and 112 acceptors  *
**
*81 donors? It should be 80 when I have 10 ligands with 8 Oh group... Am I
right?*
*112 acceptors? 7 atoms of my Glycine x 12 possibilities?*
**
*trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Will do grid-seach on 11x11x11 grid, rcut=0.35
Last frame   2000 time 10.000
Average number of hbonds per timeframe 0.642 out of 4536 possible - that
is understood = (112x81)/2*
**
*So how many possibilities has Glycine in order to create hbond? Shall I
choose just a side chain which is hydrogen?*
**
*Steven*







 Steven


 On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann 
 s.neuman...@gmail.commailto:
 s.neuman...@gmail.com** wrote:

Thank you for clarification Justin!!! The Manual is not as clear as
you :P
 Steven

On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:



Steven Neumann wrote:



On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
 mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Steven Neumann wrote:



   On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
   jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu
   mailto:jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



  Steven Neumann wrote:

  Hi Gromacs Users,
   I have calculated hydrogen bonds and
collisions between my
  ligands and every single residue using
g_hbond. Looking
   at the
  criteria adpoted by Gromacs I found impossible
that number of
  hydrogen bonds were higher than number of
collisions...
   And what
  is interesting in one of my residue I obtained
result like
  this... All Hbonds with Glycine - 1872, All
Collisions 704.
   Does anyone know how is it possible?
   I don't know how any of your
 numbers are possible
(1872 H-bonds
  forming with a glycine?), or what you are defining
as a collision
  and how you calculated it. Please provide the
exact commands that
  you're using.  If you're equating a contact (e.g.
from g_mindist)
  with a collision, then realize that the default
criteria for a
  contact are very different than the geometric
criteria for a
  hydrogen bond.

  -Justin

  -- ==**
 __==

  Justin A. Lemkul
  Ph.D. Candidate
  ICTAS Doctoral Scholar
  MILES-IGERT Trainee
  Department of Biochemistry
  Virginia Tech
  Blacksburg, VA
  jalemkul[at]vt.edu http://vt.edu/
http://vt.edu/ http://vt.edu/ | (540)

   231-9080 tel:%28540%29%20231-9080
  tel:%28540%29%20231-9080

  http://www.bevanlab.biochem
http://www.bevanlab.biochem/**.

Re: [gmx-users] g_hbond

2011-09-01 Thread Mark Abraham


On 1/09/2011 6:14 PM, Steven Neumann wrote:



On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Steven Neumann wrote:

One question for Glycine it is easy to assess 3 possible
hbonds which can create as hydrogen is only one atom as a side
chain.
How about other amino acids and their maximum hbonds they can
create?


Any OH or NH group is a donor, any lone pair is an acceptor
(though obviously not modeled explicitly in MD).  The ability of
MD force fields to agree with reality in this respect is
debatable, but should come close.

-Justin

Thank you Justin. Can you please clarify me something and tell me
whether I am wrong. This is what I obtained from calulating hbonds
between 10 ligands and Glycine. Each ligand serve 8 OH group
(flavanoid) :

/*Reading file md.tpr, VERSION 4.5.4 (single precision)
Specify 2 groups to analyze:
Group 0 (   r_96) has 7 elements* -/ this is my 
Glycine - 7 atoms (side chain - Hydrogen)
/*Group 1 (LIG) has   510 elements*-/ these are 10 
ligands, 51 atoms each, 8 OH group

/*Select a group: 0 1
Selected 0: 'r_96'
Select a group: Selected 1: 'LIG'
Checking for overlap in atoms between r_96 and LIG
Calculating hydrogen bonds between r_96 (7 atoms) and LIG (510 atoms)
Found 81 donors and 112 acceptors */
*//*
/81 donors? It should be 80 when I have 10 ligands with 8 Oh group... 
Am I right?/


You are assuming g_hbond knows what you know - that only your ligand 
hydroxyls can do effective H-bonding. However, g_hbond can only look at 
the atom names of the groups you give it. Algorithms do what you say, 
not what you mean, unfortunately. 81 = 1*1 + 8*10, since NH from glycine 
is a donor.



/112 acceptors? 7 atoms of my Glycine x 12 possibilities?/


Methylene atoms cannot accept hydrogen bonds! See g_hbond -h. N and O 
from glycine are acceptors. 112 = 2*1 + 11*10


Mark


*//*
/*trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Will do grid-seach on 11x11x11 grid, rcut=0.35
Last frame   2000 time 10.000
Average number of hbonds per timeframe 0.642 out of 4536 
possible - *that is understood = (112x81)/2/

//
/So how many possibilities has Glycine in order to create hbond? Shall 
I choose just a side chain which is hydrogen?/

//
/Steven/



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[gmx-users] g_hbond

Hi Gromacs Users,

I have calculated hydrogen bonds and collisions between my ligands and every
single residue using g_hbond. Looking at the criteria adpoted by Gromacs I
found impossible that number of hydrogen bonds were higher than number of
collisions... And what is interesting in one of my residue I obtained result
like this... All Hbonds with Glycine - 1872, All Collisions 704.

Does anyone know how is it possible?

Steven
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Re: [gmx-users] g_hbond




Steven Neumann wrote:

Hi Gromacs Users,
 
I have calculated hydrogen bonds and collisions between my ligands and 
every single residue using g_hbond. Looking at the criteria adpoted by 
Gromacs I found impossible that number of hydrogen bonds were higher 
than number of collisions... And what is interesting in one of my 
residue I obtained result like this... All Hbonds with Glycine - 1872, 
All Collisions 704.
 
Does anyone know how is it possible?
 


I don't know how any of your numbers are possible (1872 H-bonds forming with a 
glycine?), or what you are defining as a collision and how you calculated it. 
Please provide the exact commands that you're using.  If you're equating a 
contact (e.g. from g_mindist) with a collision, then realize that the default 
criteria for a contact are very different than the geometric criteria for a 
hydrogen bond.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_hbond

On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Steven Neumann wrote:

Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my ligands and
every single residue using g_hbond. Looking at the criteria adpoted by
Gromacs I found impossible that number of hydrogen bonds were higher than
number of collisions... And what is interesting in one of my residue I
obtained result like this... All Hbonds with Glycine - 1872, All Collisions
704.
Does anyone know how is it possible?

I don't know how any of your numbers are possible (1872 H-bonds forming
with a glycine?), or what you are defining as a collision and how you
calculated it. Please provide the exact commands that you're using. If
you're equating a contact (e.g. from g_mindist) with a collision, then
realize that the default criteria for a contact are very different than the
geometric criteria for a hydrogen bond.

-Justin

--
==**==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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My system is made of 10 ligands and one protein. I used command:

g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg

Where I specified in the index file two groups: 10 ligands and Glycine
residue. So I have calculated hbonds (second column) and collisions (third
column) and then I made a sum of all frames during 100 ns simualtion time
(one frame every 50 ps) obtaining 1872 hbonds and 703 collisions between
Glycine and 10 ligands. I did it with every residue to assess binding
affinity of different amino acids.
Criteria for collision is distance 3.5 A, and fo hbond distance 3.5 A and
angle. So when calcualting hbond and collisions the number of hbonds has has
to be smaller while collision takes into account hbonds as welll. I obtained
results like this for all other residues which seems to be correct. Am I
right?

Steven
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Re: [gmx-users] g_hbond




Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Steven Neumann wrote:

Hi Gromacs Users,
 I have calculated hydrogen bonds and collisions between my
ligands and every single residue using g_hbond. Looking at the
criteria adpoted by Gromacs I found impossible that number of
hydrogen bonds were higher than number of collisions... And what
is interesting in one of my residue I obtained result like
this... All Hbonds with Glycine - 1872, All Collisions 704.
 Does anyone know how is it possible?
 



I don't know how any of your numbers are possible (1872 H-bonds
forming with a glycine?), or what you are defining as a collision
and how you calculated it. Please provide the exact commands that
you're using.  If you're equating a contact (e.g. from g_mindist)
with a collision, then realize that the default criteria for a
contact are very different than the geometric criteria for a
hydrogen bond.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==__==
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My system is made of 10 ligands and one protein. I used command:
 
g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
 
Where I specified in the index file two groups: 10 ligands and Glycine 
residue. So I have calculated hbonds (second column) and collisions 
(third column) and then I made a sum of all frames during 100 ns 
simualtion time (one frame every 50 ps) obtaining 1872 hbonds and 703 
collisions between Glycine and 10 ligands. I did it with every residue 
to assess binding affinity of different amino acids.
Criteria for collision is distance 3.5 A, and fo hbond distance 3.5 A 
and angle. So when calcualting hbond and collisions the number of hbonds 
has has to be smaller while collision takes into account hbonds as 
welll. I obtained results like this for all other residues which seems 
to be correct. Am I right? 
 


No.  The second column is not inclusive of the first.  It counts the number of 
atoms that are within hydrogen bonding distance, but do not meet the criteria 
because of the angle between D-H-A.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_hbond




Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Steven Neumann wrote:

Hi Gromacs Users,
 I have calculated hydrogen bonds and collisions between my
ligands and every single residue using g_hbond. Looking at the
criteria adpoted by Gromacs I found impossible that number of
hydrogen bonds were higher than number of collisions... And what
is interesting in one of my residue I obtained result like
this... All Hbonds with Glycine - 1872, All Collisions 704.
 Does anyone know how is it possible?
 



I don't know how any of your numbers are possible (1872 H-bonds
forming with a glycine?), or what you are defining as a collision
and how you calculated it. Please provide the exact commands that
you're using.  If you're equating a contact (e.g. from g_mindist)
with a collision, then realize that the default criteria for a
contact are very different than the geometric criteria for a
hydrogen bond.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==__==
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mailto:gmx-users@gromacs.org
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My system is made of 10 ligands and one protein. I used command:
 
g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
 
Where I specified in the index file two groups: 10 ligands and Glycine 
residue. So I have calculated hbonds (second column) and collisions 
(third column) and then I made a sum of all frames during 100 ns 
simualtion time (one frame every 50 ps) obtaining 1872 hbonds and 703 
collisions between Glycine and 10 ligands. I did it with every residue 
to assess binding affinity of different amino acids.


I forgot to mention in the previous message that there is no value in summing 
the hydrogen bonds over time.  Some of those H-bonds may be distinct, and others 
may be the same H-bond that has broken and subsequently re-formed.  I doubt 
anyone would find real value in saying that 10 ligands formed 1872 H-bonds with 
glycine over a trajectory.


-Justin

Criteria for collision is distance 3.5 A, and fo hbond distance 3.5 A 
and angle. So when calcualting hbond and collisions the number of hbonds 
has has to be smaller while collision takes into account hbonds as 
welll. I obtained results like this for all other residues which seems 
to be correct. Am I right? 
 
Steven




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] g_hbond

On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Steven Neumann wrote:

On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:

Steven Neumann wrote:

Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my
ligands and every single residue using g_hbond. Looking at the
criteria adpoted by Gromacs I found impossible that number of
hydrogen bonds were higher than number of collisions... And what
is interesting in one of my residue I obtained result like
this... All Hbonds with Glycine - 1872, All Collisions 704.
Does anyone know how is it possible?

I don't know how any of your numbers are possible (1872 H-bonds
forming with a glycine?), or what you are defining as a collision
and how you calculated it. Please provide the exact commands that
you're using. If you're equating a contact (e.g. from g_mindist)
with a collision, then realize that the default criteria for a
contact are very different than the geometric criteria for a
hydrogen bond.

-Justin

-- ==**__==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080
tel:%28540%29%20231-9080

http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin

http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**__==
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My system is made of 10 ligands and one protein. I used command:
g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
Where I specified in the index file two groups: 10 ligands and Glycine
residue. So I have calculated hbonds (second column) and collisions (third
column) and then I made a sum of all frames during 100 ns simualtion time
(one frame every 50 ps) obtaining 1872 hbonds and 703 collisions between
Glycine and 10 ligands. I did it with every residue to assess binding
affinity of different amino acids.

I forgot to mention in the previous message that there is no value in
summing the hydrogen bonds over time. Some of those H-bonds may be
distinct, and others may be the same H-bond that has broken and subsequently
re-formed. I doubt anyone would find real value in saying that 10 ligands
formed 1872 H-bonds with glycine over a trajectory.

-Justin

Obviosuly, but it can provide you some information about binding affinity -
some ligands remains close to some residues longer than the others so by sum
of this values you can assess residues with higher binding affinity.

Steven

Criteria for collision is distance 3.5 A, and fo hbond distance 3.5 A and
angle. So when calcualting hbond and collisions the number of hbonds has has
to be smaller while collision takes into account hbonds as welll. I obtained
results like this for all other residues which seems to be correct. Am I
right? Steven

--
==**==

==**==
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Re: [gmx-users] g_hbond




Steven Neumann wrote:



On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Steven Neumann wrote:

   Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my
   ligands and every single residue using g_hbond. Looking
at the
   criteria adpoted by Gromacs I found impossible that number of
   hydrogen bonds were higher than number of collisions...
And what
   is interesting in one of my residue I obtained result like
   this... All Hbonds with Glycine - 1872, All Collisions 704.
Does anyone know how is it possible?
   


   I don't know how any of your numbers are possible (1872 H-bonds
   forming with a glycine?), or what you are defining as a collision
   and how you calculated it. Please provide the exact commands that
   you're using.  If you're equating a contact (e.g. from g_mindist)
   with a collision, then realize that the default criteria for a
   contact are very different than the geometric criteria for a
   hydrogen bond.

   -Justin

   -- ====

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu http://vt.edu/ http://vt.edu/ | (540)
231-9080 tel:%28540%29%20231-9080
   tel:%28540%29%20231-9080

   http://www.bevanlab.biochem.
http://www.bevanlab.biochem./vt.edu/Pages/Personal/justin
http://vt.edu/Pages/Personal/justin
   http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   ====
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 My system is made of 10 ligands and one protein. I used command:
 g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
 Where I specified in the index file two groups: 10 ligands and
Glycine residue. So I have calculated hbonds (second column) and
collisions (third column) and then I made a sum of all frames
during 100 ns simualtion time (one frame every 50 ps) obtaining
1872 hbonds and 703 collisions between Glycine and 10 ligands. I
did it with every residue to assess binding affinity of
different amino acids.


I forgot to mention in the previous message that there is no value
in summing the hydrogen bonds over time.  Some of those H-bonds may
be distinct, and others may be the same H-bond that has broken and
subsequently re-formed.  I doubt anyone would find real value in
saying that 10 ligands formed 1872 H-bonds with glycine over a
trajectory.

-Justin

Obviosuly, but it can provide you some information about binding 
affinity - some ligands remains close to some residues longer than the 
others so by sum of this values you can assess residues with higher 
binding affinity.
 


The average number of hydrogen bonds over time will tell you the same thing, 
with much greater precision.  There are a maximum number of H-bonds that glycine 
can participate in, since it only has backbone groups to contribute, so if you 
find that, on average, there are 2.5 out of a possible

Re: [gmx-users] g_hbond

Thank you for clarification Justin!!! The Manual is not as clear as you :P

Steven

On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Steven Neumann wrote:



 On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
 mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Steven Neumann wrote:

   Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my
   ligands and every single residue using g_hbond. Looking
at the
   criteria adpoted by Gromacs I found impossible that number
 of
   hydrogen bonds were higher than number of collisions...
And what
   is interesting in one of my residue I obtained result like
   this... All Hbonds with Glycine - 1872, All Collisions 704.
Does anyone know how is it possible?

   I don't know how any of your numbers are possible (1872 H-bonds
   forming with a glycine?), or what you are defining as a
 collision
   and how you calculated it. Please provide the exact commands
 that
   you're using.  If you're equating a contact (e.g. from
 g_mindist)
   with a collision, then realize that the default criteria for a
   contact are very different than the geometric criteria for a
   hydrogen bond.

   -Justin

   -- ==**==

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu http://vt.edu/ http://vt.edu/ | (540)

231-9080 tel:%28540%29%20231-9080
   tel:%28540%29%20231-9080

   http://www.bevanlab.biochem.
http://www.bevanlab.biochem./**vt.edu/Pages/Personal/**
 justin http://vt.edu/Pages/Personal/justin

 http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin


   http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin

 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 

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 My system is made of 10 ligands and one protein. I used command:
 g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
 Where I specified in the index file two groups: 10 ligands and
Glycine residue. So I have calculated hbonds (second column) and
collisions (third column) and then I made a sum of all frames
during 100 ns simualtion time (one frame every 50 ps) obtaining
1872

Re: [gmx-users] g_hbond

One question for Glycine it is easy to assess 3 possible hbonds which
can create as hydrogen is only one atom as a side chain.
How about other amino acids and their maximum hbonds they can create?

Steven

On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann s.neuman...@gmail.comwrote:

 Thank you for clarification Justin!!! The Manual is not as clear as you :P

 Steven

   On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul jalem...@vt.eduwrote:



 Steven Neumann wrote:



 On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
 mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Steven Neumann wrote:

   Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my
   ligands and every single residue using g_hbond. Looking
at the
   criteria adpoted by Gromacs I found impossible that number
 of
   hydrogen bonds were higher than number of collisions...
And what
   is interesting in one of my residue I obtained result like
   this... All Hbonds with Glycine - 1872, All Collisions 704.
Does anyone know how is it possible?

   I don't know how any of your numbers are possible (1872 H-bonds
   forming with a glycine?), or what you are defining as a
 collision
   and how you calculated it. Please provide the exact commands
 that
   you're using.  If you're equating a contact (e.g. from
 g_mindist)
   with a collision, then realize that the default criteria for a
   contact are very different than the geometric criteria for a
   hydrogen bond.

   -Justin

   -- ==**==

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu http://vt.edu/ http://vt.edu/ | (540)

231-9080 tel:%28540%29%20231-9080
   tel:%28540%29%20231-9080

   http://www.bevanlab.biochem.
http://www.bevanlab.biochem./**vt.edu/Pages/Personal/**
 justin http://vt.edu/Pages/Personal/justin

 http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin


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 My system is made of 10 ligands and one protein. I used command:
 g_hbond -f md.trr -s md.tpr -n res91.ndx -num
 91with10LIGbonds.xvg

Re: [gmx-users] g_hbond




Steven Neumann wrote:
One question for Glycine it is easy to assess 3 possible hbonds 
which can create as hydrogen is only one atom as a side chain.

How about other amino acids and their maximum hbonds they can create?
 


Any OH or NH group is a donor, any lone pair is an acceptor (though obviously 
not modeled explicitly in MD).  The ability of MD force fields to agree with 
reality in this respect is debatable, but should come close.


-Justin


Steven

On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann s.neuman...@gmail.com 
mailto:s.neuman...@gmail.com wrote:


Thank you for clarification Justin!!! The Manual is not as clear as
you :P
 
Steven


On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:



Steven Neumann wrote:



On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Steven Neumann wrote:



   On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
   jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu
   mailto:jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



  Steven Neumann wrote:

  Hi Gromacs Users,
   I have calculated hydrogen bonds and
collisions between my
  ligands and every single residue using
g_hbond. Looking
   at the
  criteria adpoted by Gromacs I found impossible
that number of
  hydrogen bonds were higher than number of
collisions...
   And what
  is interesting in one of my residue I obtained
result like
  this... All Hbonds with Glycine - 1872, All
Collisions 704.
   Does anyone know how is it possible?
 
  I don't know how any of your numbers are possible

(1872 H-bonds
  forming with a glycine?), or what you are defining
as a collision
  and how you calculated it. Please provide the
exact commands that
  you're using.  If you're equating a contact (e.g.
from g_mindist)
  with a collision, then realize that the default
criteria for a
  contact are very different than the geometric
criteria for a
  hydrogen bond.

  -Justin

  -- ==__==

  Justin A. Lemkul
  Ph.D. Candidate
  ICTAS Doctoral Scholar
  MILES-IGERT Trainee
  Department of Biochemistry
  Virginia Tech
  Blacksburg, VA
  jalemkul[at]vt.edu http://vt.edu/
http://vt.edu/ http://vt.edu/ | (540)

   231-9080 tel:%28540%29%20231-9080
  tel:%28540%29%20231-9080

  http://www.bevanlab.biochem
http://www.bevanlab.biochem/.
 
 http://www.bevanlab.biochem./__vt.edu/Pages/Personal/__justin

http://vt.edu/Pages/Personal/justin
   http://vt.edu/Pages/Personal/__justin
http://vt.edu/Pages/Personal/justin

  http://www.bevanlab.biochem.
http://www.bevanlab.biochem./vt.edu/Pages/Personal/justin
http://vt.edu/Pages/Personal/justin
 
 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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[gmx-users] g_hbond simple question

2011-08-22 Thread Yao Yao

Hi Guys,

I am using g_hbond to analyze hbond between two groups. The manual says All 
hydrogen bonds between the two groups are analyzed.
Does that mean even those hbonds do not hbond to neither of the two groups are 
still under consideration?

Thanks,

Yao
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Re: [gmx-users] g_hbond simple question

2011-08-22 Thread Justin A. Lemkul




Yao Yao wrote:

Hi Guys,

I am using g_hbond to analyze hbond between two groups. The manual says 
All hydrogen bonds between the two groups are analyzed.
Does that mean even those hbonds do not hbond to neither of the two 
groups are still under consideration?




If it doesn't form a hydrogen bond, then it's not a hydrogen bond.  A hydrogen 
bond is defined by the criteria described in the manual.  If those criteria are 
not satisfied, the group does not form a hydrogen bond with whatever other group 
is examined at that time.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_hbond

2011-06-16 Thread simon sham

Hi,
I am little confused about setting up the two groups in g_hbond.
1. Are the two groups corresponding to the donor (N) and the acceptor (O) atoms?

I want to measure the lifetime, angle and distance of the triplet N-HO 
hydrogen bond. Is this the triplet that the manual talks about?

Thanks for your insight.

Simon
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[gmx-users] g_hbond

2011-06-16 Thread simon sham

Hi,
To help clarify my previous g_hbond question, I have these two groups in my 
index file
[ a_100_a_101]  # 100 is N, #101 is H
   100 101
[ a_200 ]    # 200 is O
   200 

when I ran g_hbond, I got Found 1 donors and 2 acceptors. The part that I 
don't quite understand is why it says 2 acceptors. Did I set up the groups 
correctly?

Again, hope this clarifies my question.
Thanks for your insight.

Simon


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[gmx-users] g_hbond

2011-06-16 Thread chris . neale


From g_hbond -h

OH and NH groups are regarded as donors, O is an acceptor always, N  
is an acceptor by default, but this can be switched using -nitacc.  
Dummy hydrogen atoms are assumed to be connected to the first  
preceding non-hydrogen atom.


The two groups are to find hbonds between group A and group B. If you  
want to find hbonds within group A, then you specify an index group  
that contains group A two times.


I think that you want:

[ group ]
100 101 200

Then give group 2x as the identical index group.

PS, there were problems with g_hbond a few months ago reported on  
list, I suggest that you check to ensure that these problems were fixed.


Chris.

-- original message --

Hi,
To help clarify my previous g_hbond question, I have these two groups  
in my index file

[ a_100_a_101]  # 100 is N, #101 is H
   100 101
[ a_200 ]# 200 is O
   200

when I ran g_hbond, I got Found 1 donors and 2 acceptors. The part  
that I don't quite understand is why it says 2 acceptors. Did I set up  
the groups correctly?


Again, hope this clarifies my question.
Thanks for your insight.

Simon



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[gmx-users] g_hbond/g_sas - how is it calculated?

2011-06-08 Thread Marzinek, Jan

Hi,



I have a question related to the calculation of hydrogen bonds in Gromacs. As I 
read in Manual it comes from the distance between donor and acceptor ( = 0.35 
nm) and the angle =30 degr beween hydrogen and acceptor. The question is - why 
30 degr? How is it related to the reality?



The second thing is the claculation of the accessible surface area (g_sas) of 
the molecule for instance? It is not explained in manual and I am really 
curious how g_sas makes these calculations.

As my supervisors do not know the gromacs their questions are always about such 
details :)

However, I think it is really important to understand what you are really doing 
using commands in Gromacs which provide you with really detailed results.



Thank you in advance,



Jan


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Re: [gmx-users] g_hbond/g_sas - how is it calculated?

2011-06-08 Thread lina

On Wed, Jun 8, 2011 at 10:20 PM, Marzinek, Jan
j.marzine...@imperial.ac.uk wrote:
 Hi,



 I have a question related to the calculation of hydrogen bonds in Gromacs.
 As I read in Manual it comes from the distance between donor and acceptor (
 = 0.35 nm) and the angle =30 degr beween hydrogen and acceptor. The
 question is - why 30 degr? How is it related to the reality?

It's a default value, you can change it when you need.




 The second thing is the claculation of the accessible surface area
 (g_sas) of the molecule for instance? It is not explained in manual and I am
 really curious how g_sas makes these calculations.

 As my supervisors do not know the gromacs their questions are always about
 such details :)

 However, I think it is really important to understand what you are really
 doing using commands in Gromacs which provide you with really detailed
 results.

All I can say is that, practice and problems are a good teacher.




 Thank you in advance,



 Jan


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Best Regards,

lina
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Re: [gmx-users] g_hbond/g_sas - how is it calculated?

2011-06-08 Thread Justin A. Lemkul




Marzinek, Jan wrote:

Hi,

 

I have a question related to the calculation of hydrogen bonds in 
Gromacs. As I read in Manual it comes from the distance between donor 
and acceptor ( = 0.35 nm) and the angle =30 degr beween hydrogen and 
acceptor. The question is - why 30 degr? How is it related to the reality?


 


Hydrogen bond strength decreases with distance between the donor and acceptor 
and with deviation from linearity.  A survey of crystallographic structures 
shows that these are generally accepted criteria.  There is literature on this 
that dates back many decades.




The second thing is the claculation of the accessible surface area 
(g_sas) of the molecule for instance? It is not explained in manual and 
I am really curious how g_sas makes these calculations.




I'd suggest you look at the citation provided in the PLEASE READ AND CITE THE 
FOLLOWING REFERENCE section printed when running g_sas :)


-Justin

As my supervisors do not know the gromacs their questions are always 
about such details :)


However, I think it is really important to understand what you are 
really doing using commands in Gromacs which provide you with really 
detailed results.


 


Thank you in advance,

 


Jan

 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_hbond in 4.5.4 gives wrong output

2011-04-23 Thread Bert

Dear all,

g_hbond of gromacs4.0.7 and 4.5.4 gives different outputs in average
hbond number. Is there any fix to g_hbond of 4.5.4? Any suggestions
are appreciated.

Bests,
Bert
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Re: [gmx-users] g_hbond in 4.5.4 gives wrong output

2011-04-23 Thread Justin A. Lemkul




Bert wrote:

Dear all,

g_hbond of gromacs4.0.7 and 4.5.4 gives different outputs in average
hbond number. Is there any fix to g_hbond of 4.5.4? Any suggestions
are appreciated.



This is a known bug and is present (as far as I know) in all 4.5.x versions. 
There is no fix yet.


-Justin


Bests,
Bert


--


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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_hbond error

2011-04-13 Thread Chandan Choudhury

Hello gmx-users !!

I tried using g_hbond tool to analyse h-bonds on my system. I could
successfully execute the tool for two of my systems. But the third system
should the memory problem. Below I have pasted my command and its output.

*$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num hbnum.xvg -dist
hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0 -xvgr

No option -sel
Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision)
Specify 2 groups to analyze:
Group 0 (  System) has 95687 elements
Group 1 ( HNP) has10 elements
Group 2 (  PE) has   192 elements
Group 3 (  HP) has   216 elements
Group 4 ( CPE) has 9 elements
Group 5 ( SOL) has 95235 elements
Group 6 (  Cl) has25 elements
Group 7 ( N_H) has   126 elements
Select a group: 5
Selected 5: 'SOL'
Select a group: 7
Selected 7: 'N_H'
Checking for overlap in atoms between SOL and N_H
Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126 atoms)
Found 31795 donors and 31795 acceptors

---
Program g_hbond, VERSION 4.0.7
Source code file: smalloc.c, line: 147

Fatal error:
Not enough memory. Failed to calloc 31795 elements of size 4 for
hb-hbmap[i]
(called from file gmx_hbond.c, line 186)
---

I Solve Problems (Pulp Fiction)
: Cannot allocate memory
Making hbmap structure...*


Kindly help.

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] g_hbond

2011-04-12 Thread Erik Marklund

Interesting. I can't see why that wouldn't be possible in theory, but 
there is a part of the code that would need rewriting, however.


Erik

Nilesh Dhumal skrev 2011-04-12 04.11:

I tried to use contact and -da together with following  command

g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc   -noda   -r 0.5
-contact   -num

I am getting following error.

Fatal error:Can not analyze contact between H and A: turn off -noda

Nilesh



On Mon, April 11, 2011 5:05 pm, Nilesh Dhumal wrote:

Is it possible to find number of hydrogen bonds using g_hbond by
considering the distance between Acceptor-hydrogen instead of the distance
  between Acceptor-Donor atoms.

Nilesh


On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote:


Try the -contact option.



Erik




Nilesh Dhumal skrev 2011-04-11 17.12:



Is there any way to specify clorin and florin atoms as a receptor.



Nilesh



On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:



Nilesh Dhumal wrote:




Hello,




I am trying to calculate number of hydrogen bond (O-H---CL)in my
system.

I use the following command





g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


Output file hbnum.xvg shows zero number of hydorgen bond.




Can you tell me why its showing zero no.




A strong peak is found in rdf between H and CL at 2.0 A.





Chlorine is not considered a receptor in g_hbond.




-Justin





I am using Gromacs 4.0.7 version.






Nilesh








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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin





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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] g_hbond

Hello,

I am trying to calculate number of hydrogen bond (O-H---CL)in my system.

I use the following command


 g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


Output file hbnum.xvg shows zero number of hydorgen bond.

Can you tell me why its showing zero no.

A strong peak is found in rdf between H and CL at 2.0 A.

I am using Gromacs 4.0.7 version.



Nilesh




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Re: [gmx-users] g_hbond

2011-04-11 Thread Justin A. Lemkul




Nilesh Dhumal wrote:

Hello,

I am trying to calculate number of hydrogen bond (O-H---CL)in my system.

I use the following command


 g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


Output file hbnum.xvg shows zero number of hydorgen bond.

Can you tell me why its showing zero no.

A strong peak is found in rdf between H and CL at 2.0 A.



Chlorine is not considered a receptor in g_hbond.

-Justin


I am using Gromacs 4.0.7 version.



Nilesh






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_hbond

Is there any way to specify clorin and florin atoms as a receptor.

Nilesh

On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello,


 I am trying to calculate number of hydrogen bond (O-H---CL)in my
 system.

 I use the following command



 g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


 Output file hbnum.xvg shows zero number of hydorgen bond.


 Can you tell me why its showing zero no.


 A strong peak is found in rdf between H and CL at 2.0 A.



 Chlorine is not considered a receptor in g_hbond.


 -Justin


 I am using Gromacs 4.0.7 version.




 Nilesh






 --
 


 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


 
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 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] g_hbond

2011-04-11 Thread Justin A. Lemkul




Nilesh Dhumal wrote:

Is there any way to specify clorin and florin atoms as a receptor.



Modify the code.

-Justin


Nilesh

On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


Hello,


I am trying to calculate number of hydrogen bond (O-H---CL)in my
system.

I use the following command



g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


Output file hbnum.xvg shows zero number of hydorgen bond.


Can you tell me why its showing zero no.


A strong peak is found in rdf between H and CL at 2.0 A.



Chlorine is not considered a receptor in g_hbond.


-Justin



I am using Gromacs 4.0.7 version.




Nilesh






--



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_hbond

2011-04-11 Thread Erik Marklund


Try the -contact option.

Erik


Nilesh Dhumal skrev 2011-04-11 17.12:

Is there any way to specify clorin and florin atoms as a receptor.

Nilesh

On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:

Nilesh Dhumal wrote:


Hello,


I am trying to calculate number of hydrogen bond (O-H---CL)in my
system.

I use the following command



g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


Output file hbnum.xvg shows zero number of hydorgen bond.


Can you tell me why its showing zero no.


A strong peak is found in rdf between H and CL at 2.0 A.



Chlorine is not considered a receptor in g_hbond.


-Justin



I am using Gromacs 4.0.7 version.




Nilesh






--



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] g_hbond

Is it possible to find number of hydrogen bonds using g_hbond by
considering the distance between Acceptor-hydrogen instead of the distance
between Acceptor-Donor atoms.

Nilesh

On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote:
 Try the -contact option.


 Erik



 Nilesh Dhumal skrev 2011-04-11 17.12:

 Is there any way to specify clorin and florin atoms as a receptor.


 Nilesh


 On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:

 Nilesh Dhumal wrote:


 Hello,



 I am trying to calculate number of hydrogen bond (O-H---CL)in my
 system.

 I use the following command




 g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


 Output file hbnum.xvg shows zero number of hydorgen bond.



 Can you tell me why its showing zero no.



 A strong peak is found in rdf between H and CL at 2.0 A.



 Chlorine is not considered a receptor in g_hbond.



 -Justin



 I am using Gromacs 4.0.7 version.





 Nilesh






 --
 



 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



 
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
 Read
 http://www.gromacs.org/Support/Mailing_Lists







 --
 ---
 Erik Marklund, PhD student
 Dept. of Cell and Molecular Biology, Uppsala University.
 Husargatan 3, Box 596,75124 Uppsala, Sweden
 phone:+46 18 471 4537fax: +46 18 511 755
 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] g_hbond

2011-04-11 Thread Erik Marklund


When running g_hbond -h, I see the following, among other things:

-[no]da  bool   yes Use distance Donor-Acceptor (if TRUE) or
Hydrogen-Acceptor (FALSE)

Hope that helps.

Erik

Nilesh Dhumal skrev 2011-04-11 23.05:

Is it possible to find number of hydrogen bonds using g_hbond by
considering the distance between Acceptor-hydrogen instead of the distance
between Acceptor-Donor atoms.

Nilesh

On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote:

Try the -contact option.


Erik



Nilesh Dhumal skrev 2011-04-11 17.12:


Is there any way to specify clorin and florin atoms as a receptor.


Nilesh


On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:



Hello,



I am trying to calculate number of hydrogen bond (O-H---CL)in my
system.

I use the following command




g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


Output file hbnum.xvg shows zero number of hydorgen bond.



Can you tell me why its showing zero no.



A strong peak is found in rdf between H and CL at 2.0 A.




Chlorine is not considered a receptor in g_hbond.



-Justin




I am using Gromacs 4.0.7 version.





Nilesh







--




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] g_hbond