[gmx-users] g_hbond
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Sat Jul 11 14:43:46 CEST 2015
Hello Erik,
I did the same.
Thanks,
Nilesh
> Hi Nilesh,
>
> You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the
> contacts in the last column of hb.xvg.
>
> Kind regards,
> Erik
>
>> On 10 Jul 2015, at 15:58, Nilesh Dhumal <ndhumal at andrew.cmu.edu> wrote:
>>
>> 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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>>>>>>>>>
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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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