[gmx-users] g_hbond

Fri Jul 10 16:58:40 CEST 2015

I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm?

Nilesh

> 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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