Re: [gmx-users] gmx hbond query

[Najamuddin Memon]

Make index of water mediated hydrogens and DNA bases so that DNA bases are
in separate group and water mediated hydrogens in separate group in drop
down menu

On Thu, May 9, 2019, 11:54 AM  wrote:

> Dear all
> I want to determine the water mediated hydrogen between DNA bases and
> small molecule. What extra flag should I use in gmx hbond command? Is
> there any other option to capture the water mediated Hbonds? Please
> suggest something.
> Sunipa Sarkar
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Re: [gmx-users] gmx hbond

[Smith, Micholas D.]

You could use gmx select to create an index file containing water molecules 
obeying these criteria at each time-step, and then use gmx hbond for for each 
index (being sure to only look at the relevant frame only).


Something like this:


gmx select (your commands here to generate an index index file for each frame).


Then use a loop like so:

#where I assume index 0 is the amino acid you are interested in


for((i=1;i<$MAXFRAMES_SELECTION;i++)); do

echo "0 \r $i" | gmx hbonds -num -r 0.2 -b "$i" -e "$i"  -n 
index_file_containing_waters_at_2Ang_at_each_frame.ndx; sed -e '/\#/d' - 
'/\@/d' -e '/\&/d' hbnum.xvg >>hbnum_2Ang.dat; rm hbnum.xvg ;done


Make a new index file for the 0.2 to 0.4 Ang and repeat.


-Micholas


===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of paul buscemi 

Sent: Sunday, January 6, 2019 12:41:41 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx hbond

Use VMD/extensions/hydrogen bonds

> On Jan 6, 2019, at 11:01 AM, rose rahmani  wrote:
>
> hi,
>
> I want to know the number of hydrogen bonds of amino acid with water in
> different distances above surface. for example in first 0.2nm, in second
> 0.2 nm(0.2-0.4 nm) above surface. how can i do it by gmx hbond? I couldn't
> find any proper option for that.
>
> best
> --
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Re: [gmx-users] gmx hbond

[rose rahmani]

Thank you. But it just adjusts the cut-off between atoms not the number of
hydrogen bonds in a given distance above the surface (or in the box). would
you please help me?

Best

On Sun, Jan 6, 2019 at 9:12 PM paul buscemi  wrote:

> Use VMD/extensions/hydrogen bonds
>
> > On Jan 6, 2019, at 11:01 AM, rose rahmani  wrote:
> >
> > hi,
> >
> > I want to know the number of hydrogen bonds of amino acid with water in
> > different distances above surface. for example in first 0.2nm, in second
> > 0.2 nm(0.2-0.4 nm) above surface. how can i do it by gmx hbond? I
> couldn't
> > find any proper option for that.
> >
> > best
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> send a mail to gmx-users-requ...@gromacs.org.
>
> --
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Re: [gmx-users] gmx hbond

[paul buscemi]

Use VMD/extensions/hydrogen bonds

> On Jan 6, 2019, at 11:01 AM, rose rahmani  wrote:
> 
> hi,
> 
> I want to know the number of hydrogen bonds of amino acid with water in
> different distances above surface. for example in first 0.2nm, in second
> 0.2 nm(0.2-0.4 nm) above surface. how can i do it by gmx hbond? I couldn't
> find any proper option for that.
> 
> best
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
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Re: [gmx-users] Gmx hbond

[Justin Lemkul]

On 4/13/18 2:22 AM, rose rahmani wrote:

Hi,

I have 2 questions, but please consider them 2 distinct questions and are
not related.
I did umbrella sapmling and calculate the PMF.
Now i I want to calculate number of hydrogen bonds for amino acid in its
initial distance(far from surface) and binding distance ( which is close to
surface and PMF is minimum there).
1- Is it rational to use pulling data(traj.xtc, .tpr,...) to calculate this
analysis, as it is nonequilibrium condition?


Sure. In each umbrella sampling window, you're restricting motion along 
a reaction coordinate, which allows you exactly compute 
distance-dependent properties.



2- Is it better to choose initial frame and binding frame, do umbrella
sampling step (, nvt) and calculate number of hbons separately and compare
the result? Is it true to compare them in this condition?


Using only the starting frame makes no sense. There's no reason to think 
that any single frame from any simulation is representative of the 
actual ensemble.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] GMX hbond

[Justin Lemkul]

On 4/10/18 6:49 PM, Dhumal, Nilesh wrote:

I defined donor and hydrogen both in donor group. Acceptors are in acceptor 
group.


The code does not find valid donors and acceptors. Donors are NH and OH, 
acceptors are N and O. You'd have to modify the code to get anything 
else to work.


-Justin


Nilesh

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, April 10, 2018 6:45:07 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond



On 4/10/18 6:43 PM, Dhumal, Nilesh wrote:

I tried, didn't find the proper answer. I run the simulation using Gromacs 4.5 
version and used g_hbond successfully.  Could not find out why its not working 
using gmx hbond.

No version of GROMACS should have ever worked with such index groups.

A hydrogen bond must be defined by at least three atoms, because it is
based on both the D-A distance and the D-H-A angle. One cannot do the
analysis on a group that contains only H atoms. Your donors have to
include both D and H atoms, and the acceptor group the A atoms.

-Justin


Nilesh


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, April 10, 2018 6:39:37 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond



On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:

Hello Gromacs users,


I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION 
5.1.4. I did following steps

mx hbond -f traj.trr -s md.tpr -n index.ndx -ac

Reading file md.tpr, VERSION 5.1.4 (single precision)
Specify 2 groups to analyze:
Group 0 ( System) has  2560 elements
Group 1 (  Other) has  2432 elements
Group 2 (EMI) has  2432 elements
Group 3 ( CL) has   128 elements
Group 4 (Ion) has   128 elements
Group 5 (EMI) has  2432 elements
Group 6 ( CL) has   128 elements
Group 7 (  C) has   128 elements
Group 8 ( C2) has   128 elements
Group 9 ( C4) has   128 elements
Group10 ( H9) has   128 elements
Group11 (H10) has   128 elements
Group12 (H11) has   128 elements
Group13 ( CL) has   128 elements
Group14 ( ch) has   256 elements
Group15 ( ch) has 3 elements
Group16 ( O1) has 2 elements
Select a group: 14
Selected 14: 'ch'
Select a group: 13
Selected 13: 'CL'
Checking for overlap in atoms between ch and CL
Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms)
Found 0 donors and 0 acceptors
Making hbmap structure...done.
No Donors or Acceptors found

---
Program gmx hbond, VERSION 5.1.4
Source code file: /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, 
l   
   ine: 3984

Fatal error:
Nothing to be done
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Group 14 is list of donor hydrogen (eg. 4(donor) 11(hydrogen)) and group is 
list of acceptors . Why donors and acceptors are zero.

Have you tried Googling the error? The first result has the answer...

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department 

Re: [gmx-users] GMX hbond

[Dhumal, Nilesh]

I defined donor and hydrogen both in donor group. Acceptors are in acceptor 
group.

Nilesh

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, April 10, 2018 6:45:07 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond



On 4/10/18 6:43 PM, Dhumal, Nilesh wrote:
> I tried, didn't find the proper answer. I run the simulation using Gromacs 
> 4.5 version and used g_hbond successfully.  Could not find out why its not 
> working using gmx hbond.

No version of GROMACS should have ever worked with such index groups.

A hydrogen bond must be defined by at least three atoms, because it is
based on both the D-A distance and the D-H-A angle. One cannot do the
analysis on a group that contains only H atoms. Your donors have to
include both D and H atoms, and the acceptor group the A atoms.

-Justin

> Nilesh
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Justin 
> Lemkul 
> Sent: Tuesday, April 10, 2018 6:39:37 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] GMX hbond
>
>
>
> On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:
>> Hello Gromacs users,
>>
>>
>> I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION 
>> 5.1.4. I did following steps
>>
>> mx hbond -f traj.trr -s md.tpr -n index.ndx -ac
>>
>> Reading file md.tpr, VERSION 5.1.4 (single precision)
>> Specify 2 groups to analyze:
>> Group 0 ( System) has  2560 elements
>> Group 1 (  Other) has  2432 elements
>> Group 2 (EMI) has  2432 elements
>> Group 3 ( CL) has   128 elements
>> Group 4 (Ion) has   128 elements
>> Group 5 (EMI) has  2432 elements
>> Group 6 ( CL) has   128 elements
>> Group 7 (  C) has   128 elements
>> Group 8 ( C2) has   128 elements
>> Group 9 ( C4) has   128 elements
>> Group10 ( H9) has   128 elements
>> Group11 (H10) has   128 elements
>> Group12 (H11) has   128 elements
>> Group13 ( CL) has   128 elements
>> Group14 ( ch) has   256 elements
>> Group15 ( ch) has 3 elements
>> Group16 ( O1) has 2 elements
>> Select a group: 14
>> Selected 14: 'ch'
>> Select a group: 13
>> Selected 13: 'CL'
>> Checking for overlap in atoms between ch and CL
>> Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms)
>> Found 0 donors and 0 acceptors
>> Making hbmap structure...done.
>> No Donors or Acceptors found
>>
>> ---
>> Program gmx hbond, VERSION 5.1.4
>> Source code file: 
>> /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, l   
>>  
>>   ine: 3984
>>
>> Fatal error:
>> Nothing to be done
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> Group 14 is list of donor hydrogen (eg. 4(donor) 11(hydrogen)) and group 
>> is list of acceptors . Why donors and acceptors are zero.
> Have you tried Googling the error? The first result has the answer...
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing li

Re: [gmx-users] GMX hbond

[Justin Lemkul]

On 4/10/18 6:43 PM, Dhumal, Nilesh wrote:

I tried, didn't find the proper answer. I run the simulation using Gromacs 4.5 
version and used g_hbond successfully.  Could not find out why its not working 
using gmx hbond.


No version of GROMACS should have ever worked with such index groups.

A hydrogen bond must be defined by at least three atoms, because it is 
based on both the D-A distance and the D-H-A angle. One cannot do the 
analysis on a group that contains only H atoms. Your donors have to 
include both D and H atoms, and the acceptor group the A atoms.


-Justin


Nilesh


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, April 10, 2018 6:39:37 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond



On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:

Hello Gromacs users,


I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION 
5.1.4. I did following steps

mx hbond -f traj.trr -s md.tpr -n index.ndx -ac

Reading file md.tpr, VERSION 5.1.4 (single precision)
Specify 2 groups to analyze:
Group 0 ( System) has  2560 elements
Group 1 (  Other) has  2432 elements
Group 2 (EMI) has  2432 elements
Group 3 ( CL) has   128 elements
Group 4 (Ion) has   128 elements
Group 5 (EMI) has  2432 elements
Group 6 ( CL) has   128 elements
Group 7 (  C) has   128 elements
Group 8 ( C2) has   128 elements
Group 9 ( C4) has   128 elements
Group10 ( H9) has   128 elements
Group11 (H10) has   128 elements
Group12 (H11) has   128 elements
Group13 ( CL) has   128 elements
Group14 ( ch) has   256 elements
Group15 ( ch) has 3 elements
Group16 ( O1) has 2 elements
Select a group: 14
Selected 14: 'ch'
Select a group: 13
Selected 13: 'CL'
Checking for overlap in atoms between ch and CL
Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms)
Found 0 donors and 0 acceptors
Making hbmap structure...done.
No Donors or Acceptors found

---
Program gmx hbond, VERSION 5.1.4
Source code file: /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, 
l   
   ine: 3984

Fatal error:
Nothing to be done
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Group 14 is list of donor hydrogen (eg. 4(donor) 11(hydrogen)) and group is 
list of acceptors . Why donors and acceptors are zero.

Have you tried Googling the error? The first result has the answer...

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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mail to gmx-users-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] GMX hbond

[Dhumal, Nilesh]

I tried, didn't find the proper answer. I run the simulation using Gromacs 4.5 
version and used g_hbond successfully.  Could not find out why its not working 
using gmx hbond.

Nilesh


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, April 10, 2018 6:39:37 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond



On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:
> Hello Gromacs users,
>
>
> I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION 
> 5.1.4. I did following steps
>
> mx hbond -f traj.trr -s md.tpr -n index.ndx -ac
>
> Reading file md.tpr, VERSION 5.1.4 (single precision)
> Specify 2 groups to analyze:
> Group 0 ( System) has  2560 elements
> Group 1 (  Other) has  2432 elements
> Group 2 (EMI) has  2432 elements
> Group 3 ( CL) has   128 elements
> Group 4 (Ion) has   128 elements
> Group 5 (EMI) has  2432 elements
> Group 6 ( CL) has   128 elements
> Group 7 (  C) has   128 elements
> Group 8 ( C2) has   128 elements
> Group 9 ( C4) has   128 elements
> Group10 ( H9) has   128 elements
> Group11 (H10) has   128 elements
> Group12 (H11) has   128 elements
> Group13 ( CL) has   128 elements
> Group14 ( ch) has   256 elements
> Group15 ( ch) has 3 elements
> Group16 ( O1) has 2 elements
> Select a group: 14
> Selected 14: 'ch'
> Select a group: 13
> Selected 13: 'CL'
> Checking for overlap in atoms between ch and CL
> Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms)
> Found 0 donors and 0 acceptors
> Making hbmap structure...done.
> No Donors or Acceptors found
>
> ---
> Program gmx hbond, VERSION 5.1.4
> Source code file: 
> /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, l
>   
> ine: 3984
>
> Fatal error:
> Nothing to be done
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Group 14 is list of donor hydrogen (eg. 4(donor) 11(hydrogen)) and group 
> is list of acceptors . Why donors and acceptors are zero.

Have you tried Googling the error? The first result has the answer...

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] GMX hbond

[Justin Lemkul]

On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:

Hello Gromacs users,


I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION 
5.1.4. I did following steps

mx hbond -f traj.trr -s md.tpr -n index.ndx -ac

Reading file md.tpr, VERSION 5.1.4 (single precision)
Specify 2 groups to analyze:
Group 0 ( System) has  2560 elements
Group 1 (  Other) has  2432 elements
Group 2 (EMI) has  2432 elements
Group 3 ( CL) has   128 elements
Group 4 (Ion) has   128 elements
Group 5 (EMI) has  2432 elements
Group 6 ( CL) has   128 elements
Group 7 (  C) has   128 elements
Group 8 ( C2) has   128 elements
Group 9 ( C4) has   128 elements
Group10 ( H9) has   128 elements
Group11 (H10) has   128 elements
Group12 (H11) has   128 elements
Group13 ( CL) has   128 elements
Group14 ( ch) has   256 elements
Group15 ( ch) has 3 elements
Group16 ( O1) has 2 elements
Select a group: 14
Selected 14: 'ch'
Select a group: 13
Selected 13: 'CL'
Checking for overlap in atoms between ch and CL
Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms)
Found 0 donors and 0 acceptors
Making hbmap structure...done.
No Donors or Acceptors found

---
Program gmx hbond, VERSION 5.1.4
Source code file: /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, 
l   
   ine: 3984

Fatal error:
Nothing to be done
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Group 14 is list of donor hydrogen (eg. 4(donor) 11(hydrogen)) and group is 
list of acceptors . Why donors and acceptors are zero.


Have you tried Googling the error? The first result has the answer...

-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] gmx hbond

[Erik Marklund]

Hi Negar,

Correct, the -dist option doesn’t do what you want it to. I cannot come up with 
a recipe for how to do this, but I suspect multiple rounds of gmx select and 
gmx hbond might do the trick.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 5 Feb 2018, at 15:49, negar habibzadeh 
mailto:negar...@gmail.com>> wrote:

Hi

I want to calculate *number of hydrogen bond* by *distance from center of
bilayer*.
i use gmx hbonds -dist but it doesn't give me the proper 
result.is it true?
which options should i implement to get the best result?

best regads
-negar
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Re: [gmx-users] Gmx hbond

[Justin Lemkul]

On 8/6/17 4:21 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi justin
Thank you for your replyingBut you said in this tuturial, in order to have tc_groups = protein non-protein , it is best to consider protein and ligand as one single entity. So we use make-ndx to merg them. When i issue 


...for the purpose of thermostatting, nothing else.  Again, merging two groups 
doesn't eliminate either from the list unless you actually deleted them.


gmx hbond there isnt any ligand in this list to choose. How can i determine h 
bonds between protein and ligan , even in my project that is about HDAC2 and my 
designed drug


If you're working on a different system, you're not going to have the exact same 
options as in my tutorial.  Likely your ligand isn't called "JZ4," so look for 
something else that makes sense for your system.


-Justin


Thank you Farial



Sent from Yahoo Mail for iPhone


On Sunday, August 6, 2017, 5:06 AM, Justin Lemkul  wrote:



On 8/4/17 11:13 AM, farial tavakoli wrote:

   blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs user
I am performing protein ligand complex (t4lysosim) and now i need to analyze JZ4 hydrogen bonding, 
but when i type Gmx hbondThere is no JZ4 in the list to choose. It is because of i used :Gmx 
make_ndx -f em.gro -o index.ndxAnd merged the " protein " and " JZ4" groupsIs 
there anyone help me how to check the hydrogen bond of JZ4 ligand?


Both protein and ligand are default groups and do not require the use of an
index file.  If the ligand isn't showing up in the list, it's probably because
you're supplying an index file from which the ligand group has been deleted.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Gmx hbond

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi justin
Thank you for your replyingBut you said in this tuturial, in order to have 
tc_groups = protein non-protein , it is best to consider protein and ligand as 
one single entity. So we use make-ndx to merg them. When i issue gmx hbond 
there isnt any ligand in this list to choose. How can i determine h bonds 
between protein and ligan , even in my project that is about HDAC2 and my 
designed drug
Thank you Farial



Sent from Yahoo Mail for iPhone


On Sunday, August 6, 2017, 5:06 AM, Justin Lemkul  wrote:



On 8/4/17 11:13 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear gromacs user
> I am performing protein ligand complex (t4lysosim) and now i need to analyze 
> JZ4 hydrogen bonding, but when i type Gmx hbondThere is no JZ4 in the list to 
> choose. It is because of i used :Gmx make_ndx -f em.gro -o index.ndxAnd 
> merged the " protein " and " JZ4" groupsIs there anyone help me how to check 
> the hydrogen bond of JZ4 ligand?

Both protein and ligand are default groups and do not require the use of an 
index file.  If the ligand isn't showing up in the list, it's probably because 
you're supplying an index file from which the ligand group has been deleted.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Gmx hbond

[Justin Lemkul]

On 8/4/17 11:13 AM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs user
I am performing protein ligand complex (t4lysosim) and now i need to analyze JZ4 hydrogen bonding, 
but when i type Gmx hbondThere is no JZ4 in the list to choose. It is because of i used :Gmx 
make_ndx -f em.gro -o index.ndxAnd merged the " protein " and " JZ4" groupsIs 
there anyone help me how to check the hydrogen bond of JZ4 ligand?


Both protein and ligand are default groups and do not require the use of an 
index file.  If the ligand isn't showing up in the list, it's probably because 
you're supplying an index file from which the ligand group has been deleted.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] gmx hbond -tu error

[Mark Abraham]

Hi,

A quick glance at the code suggests Justin is right. You should be able to
inspect the output of gmx hbond and see that in fact -e means that many
fewer trajectory frames are being read.

Mark

On Tue, May 2, 2017 at 2:56 AM Justin Lemkul  wrote:

>
>
> On 5/1/17 10:15 AM, Marcelo Depólo wrote:
> > Hi!
> >
> >
> > I am running ACF calculations in gmx hbond tool in 5.0.7 version.
> >
> > When running:
> >
> > gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg
> >
> > and
> >
> > gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg
> >
> >
> > The results given for the ACF are completely different (example: CHI^2 =
> > 0.000347 and CHI^2 = 22.9131, respectively). It seems -tu flag is not
> > working properly here.
> >
> > Still, all graphs generated make sense (going until 5ns, the half of
> > trajectory time analyzed).
> >
> > Does anyone already encountered this error?
> >
>
> The -tu option only alters output time values, not the arguments on the
> command
> line, IIRC.  The help info does specify that -b and -e take time in ps.
> This is
> somewhat non-intuitive, but the behavior is consistent with the
> documentation.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] gmx hbond -tu error

[Justin Lemkul]

On 5/1/17 10:15 AM, Marcelo Depólo wrote:

Hi!


I am running ACF calculations in gmx hbond tool in 5.0.7 version.

When running:

gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg

and

gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg


The results given for the ACF are completely different (example: CHI^2 =
0.000347 and CHI^2 = 22.9131, respectively). It seems -tu flag is not
working properly here.

Still, all graphs generated make sense (going until 5ns, the half of
trajectory time analyzed).

Does anyone already encountered this error?



The -tu option only alters output time values, not the arguments on the command 
line, IIRC.  The help info does specify that -b and -e take time in ps.  This is 
somewhat non-intuitive, but the behavior is consistent with the documentation.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] gmx hbond

[Mohsen Ramezanpour]

Thanks Erik, It helped.

Cheers

On Sat, Apr 15, 2017 at 9:30 AM, Erik Marklund 
wrote:

> Dear Moshen,
>
> I doubt the difference in versions will cause any problems in this case.
>
> The second column is ill-described. It contains the number of pairs within
> 0.3 nm that don’t fulfil the angle criterion.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 14 Apr 2017, at 03:20, Mohsen Ramezanpour  > wrote:
>
> Hi Gromacs users,
>
> I have a question regarding the output file from g_hbond:
>
> First:I have done my simulations with version 4.6.7 and doing the analysis
> with version 2016.2
> Will this cause any hidden problem in analysis? the analysis is working
> fine but I am asking about the correctness of results because of this
> change.
>
>
> Second and the main question:
>
> When I use this command:
> gmx hbond -f md.xtc -n index.ndx -s  file.tpr -num hbond.xvg -g test.log -r
> 0.30
>
> I get this:
>
> ...
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.3 nm"
>400   0
> *  40.1   1   0*
>  40.2   1   3
>  40.3   2   2
>  40.4   0   2
>  40.5   1   1
> *  40.6   2   0*
> ...
> the first column is time frame
> the second is number of h-bonds
> the third is "Pairs within 0.3 nm"
>
>
> by -r 0.30 I wanted to change the cut-off for h-bond definition.
> i.e. report a h-bond if and only if the D...A distance is less or equal to
> 0.30 ns, AND, the angle of H..D...A is less or equal than 35 (this angle is
> default in 2016.2 version).
>
> Regarding the highlighted lines:
> How it is possible that the there is not any pair in this distance but we
> still have hbond?
> If they are not in this cut-off, thy should not be recognized as hbond
> either.
>
> I assume the pair means the D...A pair because I did NOT use -noda  option.
>
> Also, it does not give any test.log file, and other problems :-)
>
> Please let me know your opinion about this results.
>
> Thanks in advance for your reply
> Cheers
> Mohsen
>
>
> --
> *Rewards work better than punishment ...*
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Re: [gmx-users] gmx hbond

[Erik Marklund]

Dear Moshen,

I doubt the difference in versions will cause any problems in this case.

The second column is ill-described. It contains the number of pairs within 0.3 
nm that don’t fulfil the angle criterion.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 14 Apr 2017, at 03:20, Mohsen Ramezanpour 
mailto:ramezanpour.moh...@gmail.com>> wrote:

Hi Gromacs users,

I have a question regarding the output file from g_hbond:

First:I have done my simulations with version 4.6.7 and doing the analysis
with version 2016.2
Will this cause any hidden problem in analysis? the analysis is working
fine but I am asking about the correctness of results because of this
change.


Second and the main question:

When I use this command:
gmx hbond -f md.xtc -n index.ndx -s  file.tpr -num hbond.xvg -g test.log -r
0.30

I get this:

...
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.3 nm"
   400   0
*  40.1   1   0*
 40.2   1   3
 40.3   2   2
 40.4   0   2
 40.5   1   1
*  40.6   2   0*
...
the first column is time frame
the second is number of h-bonds
the third is "Pairs within 0.3 nm"


by -r 0.30 I wanted to change the cut-off for h-bond definition.
i.e. report a h-bond if and only if the D...A distance is less or equal to
0.30 ns, AND, the angle of H..D...A is less or equal than 35 (this angle is
default in 2016.2 version).

Regarding the highlighted lines:
How it is possible that the there is not any pair in this distance but we
still have hbond?
If they are not in this cut-off, thy should not be recognized as hbond
either.

I assume the pair means the D...A pair because I did NOT use -noda  option.

Also, it does not give any test.log file, and other problems :-)

Please let me know your opinion about this results.

Thanks in advance for your reply
Cheers
Mohsen


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Re: [gmx-users] gmx hbond - specify precise atom names involved

[Erik Marklund]

Hi,

Not as of yet I’m afraid.

Erik

> On 3 May 2016, at 08:16, Nash, Anthony  wrote:
> 
> 
> Hi all,
> 
> Can gmx hbond accept user specified atoms for the donors (default OH and
> NH) and acceptor (default O and N)? I don¹t seem to find any mention of
> this in the -help text.
> 
> I have a post-trans modified protein from a rather bulk cross-linked
> peptide chain. I defined unique atom times but I have used a unique set of
> atom names. 
> 
> Thanks
> Anthony 
> 
> 
> 
> 
>> 
> 
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Re: [gmx-users] gmx hbond - specify precise atom names involved

[Justin Lemkul]

On 5/3/16 5:21 PM, Nash, Anthony wrote:

Thanks Justin,


I’ll give that a try. I assume this approach would still require the .trr
to be converted to a .gro file, and then the customised names
‘search-replaced’ with the respective ‘fake’ names?



No.  Names are read from the reference coordinates and nothing else (since 
trajectories don't have atom name information, anyway).


-Justin


Thanks
Anthony

On 03/05/2016 16:22, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Justin Lemkul"
 wrote:




On 5/3/16 9:16 AM, Nash, Anthony wrote:


Hi all,

Can gmx hbond accept user specified atoms for the donors (default OH and
NH) and acceptor (default O and N)? I don¹t seem to find any mention of
this in the -help text.



It's hard-coded in the source, so it's rather inflexible.


I have a post-trans modified protein from a rather bulk cross-linked
peptide chain. I defined unique atom times but I have used a unique set
of
atom names.



Create a "fake" topology that uses O,N,H as the first character in
applicable
atom names.  Then run the analysis using this .tpr file.  We did this a
while
back with, e.g. thiols and a few others.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] gmx hbond - specify precise atom names involved

[Nash, Anthony]

Thanks Justin,


I’ll give that a try. I assume this approach would still require the .trr
to be converted to a .gro file, and then the customised names
‘search-replaced’ with the respective ‘fake’ names?

Thanks
Anthony

On 03/05/2016 16:22, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Justin Lemkul"
 wrote:

>
>
>On 5/3/16 9:16 AM, Nash, Anthony wrote:
>>
>> Hi all,
>>
>> Can gmx hbond accept user specified atoms for the donors (default OH and
>> NH) and acceptor (default O and N)? I don¹t seem to find any mention of
>> this in the -help text.
>>
>
>It's hard-coded in the source, so it's rather inflexible.
>
>> I have a post-trans modified protein from a rather bulk cross-linked
>> peptide chain. I defined unique atom times but I have used a unique set
>>of
>> atom names.
>>
>
>Create a "fake" topology that uses O,N,H as the first character in
>applicable 
>atom names.  Then run the analysis using this .tpr file.  We did this a
>while 
>back with, e.g. thiols and a few others.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>send a mail to gmx-users-requ...@gromacs.org.

-- 
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Re: [gmx-users] gmx hbond - specify precise atom names involved

[Justin Lemkul]

On 5/3/16 9:16 AM, Nash, Anthony wrote:


Hi all,

Can gmx hbond accept user specified atoms for the donors (default OH and
NH) and acceptor (default O and N)? I don¹t seem to find any mention of
this in the -help text.



It's hard-coded in the source, so it's rather inflexible.


I have a post-trans modified protein from a rather bulk cross-linked
peptide chain. I defined unique atom times but I have used a unique set of
atom names.



Create a "fake" topology that uses O,N,H as the first character in applicable 
atom names.  Then run the analysis using this .tpr file.  We did this a while 
back with, e.g. thiols and a few others.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

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