[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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: Tuesday, April 10, 2018 6:45:07 PM
> To: gmx-users at 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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
>> Sent: Tuesday, April 10, 2018 6:39:37 PM
>> To: gmx-users at 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
>>> Group    10 (             H9) has   128 elements
>>> Group    11 (            H10) has   128 elements
>>> Group    12 (            H11) has   128 elements
>>> Group    13 (             CL) has   128 elements
>>> Group    14 (             ch) has   256 elements
>>> Group    15 (             ch) has     3 elements
>>> Group    16 (             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
>>
>> jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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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

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

==================================================