[gmx-users] Protein-Protein distance

[Life Sciences Inc]

OK , Thanks a lot now I got  it , if I feel any difficulty further I will
ask.

Thank you



On Wed, Jan 6, 2016 at 2:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/5/16 4:11 PM, Life Sciences Inc wrote:
>
>> I am little confued to use the gmx distance command specifically for my
>> purpose mentioned in my question ;
>>
>> gmx distance -f file.xtc -s file.gro -n file.ndx
>>
>> for outputting the distance between protein 1 and protein 2, protein 1 and
>> protein 3 , protein 1 and protein 4 I will use -oav or -oxyz or -oall
>> option ?and how can I calculate the distance between the proteins with
>> center of mass of my selection which I am providing though index file?
>>
>>
> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist
>
> Read the help description to see which of the available output options you
> need; they all provide slightly different content.  If you just want the
> total distance, use -oall, for the (x,y,z) components, use -oxyz.
>
> The actual selection string you need to pass to -select (or choose
> interactively, as would be the case for the command you have shown) depends
> on what the groups are named/numbered in the index file.
>
> If you have, e.g. groups "protein1" and "protein2":
>
> gmx distance -f file.xtc -s file.gro -n file.ndx -selet 'com of group
> "protein1" plus com of group "protein2"'
>
> -Justin
>
>
>
>>
>> On Tue, Jan 5, 2016 at 5:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/5/16 1:18 AM, Life Sciences Inc wrote:
>>>
>>> Dear Gromacs Users
>>>>
>>>> Kindly let me know how to calculate the protein protein distance as a
>>>> function of time with gromacs. I want to calculate the distance based on
>>>> the center of mass of the selection which is CA atoms. I have 4 proteins
>>>> in
>>>> the system and want to calculate the distances as distance between
>>>> Protein
>>>> 1 and Protein 2, then Protein 1 and Protein 3 , then Protein 1 and
>>>> Protein
>>>> 4.
>>>>
>>>>
>>>> I used gmx mindist command but it cannot be used to calculate distance
>>>> with
>>>> center of mass, I tried gmx distance also, but do not know how to use it
>>>> for my above mentioned purpose.
>>>>
>>>>
>>>> gmx distance is the correct command, but you haven't told us what you've
>>> tried and why it didn't work (or why you think it didn't work), so it's
>>> not
>>> productive for us to simply guess.
>>>
>>> -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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> Gromacs Users mailing list
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