[gmx-users] g_hbond

[Erik Marklund]

But without contact you will need a full donor-hydrogen-acceptor triad for it to be registered, which is not what you want as far as I can tell.

Erik

> On 10 Jul 2015, at 15:17, Nilesh Dhumal <ndhumal at andrew.cmu.edu> wrote:
> 
> This is index file
> 
> [ O8-H18-1 ]
>   8  18
> [ O8-H18-2 ]
> 4032
> 
> 
> Found 1 donors and 2 acceptors
> 
> Its look contact YES check the distance between accetpr---donor.
> 
> I will run without contact.
> 
> Nilesh
> 
>> Hi Nilesh,
>> 
>> Am not sure it accepts hydrogens as donors/acceptors even with -contact.
>> How many donors and acceptors are found?
>> 
>> Kind regards,
>> Erik
>> 
>>> On 10 Jul 2015, at 14:37, Nilesh Dhumal <ndhumal at andrew.cmu.edu> wrote:
>>> 
>>> I calculated number of hydrogen bond with cutoff 0.25 nm (Distance
>>> between
>>> hydrogen and O,acceptor) using g_hbond,
>>> 
>>> g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg
>>> -nonitacc
>>> -r 0.25 -contact -dist
>>> 
>>> The found the calculated number of hydrogen bond along time are zero and
>>> -nan is the in hbdist.xvg file.
>>> I calculated the distance between hydrogen and oxygen using g_dist and
>>> the
>>> calculated the distance is less than 0.25 nm.
>>> 
>>> Why am I getting zero number of hydrogen bonds using g_hbond (based on
>>> same cutoff )?
>>> 
>>> Nilesh
>>> 
>>> 
>>> 
>>>> Thanks.
>>>> 
>>>> I will use two groups.
>>>> 
>>>> Nilesh
>>>>> 
>>>>> On 7/9/15 9:13 PM, Nilesh Dhumal wrote:
>>>>>>> 
>>>>>>> 
>>>>>>> On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
>>>>>>>> Hello,
>>>>>>>> 
>>>>>>>> I am calculating g_hbond for water system.  I have a question about
>>>>>>>> specifying two group for calculating hydrogen bond.
>>>>>>>> 
>>>>>>>> Do I specify atoms in triplet(O-H---O)?
>>>>>>>> Can I specify O-H as one group (Donor-Hydrogen) and O in other
>>>>>>>> group
>>>>>>>> (Acceptor)?
>>>>>>> 
>>>>>>> If the system is pure water, you do not need any special index
>>>>>>> groups.
>>>>>> 
>>>>>> I have DMSO in the system. I just mentioned water to make it simple.
>>>>>> I am interested in O--H---O(DMSO) interactions?
>>>>>> 
>>>>>> How should I specify this?
>>>>>> 
>>>>>> With one triplet O--H---O(DMSO) or two groups one O--H and second
>>>>>> O(DMSO)
>>>>> 
>>>>> The latter - just use DMSO and water groups.  O can be a donor or
>>>>> acceptor, and
>>>>> g_hbond intelligently figures out whether or not a given atom is a
>>>>> donor
>>>>> or
>>>>> acceptor (or both).
>>>>> 
>>>>> -Justin
>>>>> 
>>>>>>> 
>>>>>>>> Default  -r cutoff is 0.35nm. Is the distance between
>>>>>>>> hydrogen---acceptor
>>>>>>>> or distance between donor---acceptor?
>>>>>>> 
>>>>>>> Read the first sentence of the help description.
>>>>>>> 
>>>>>>> -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
>>>>>>> 
>>>>>>> jalemkul at 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
>>>>> 
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>> 
>>>>> ==================================================
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>>>> 
>>>> 
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