[gmx-users] Re: Salt bridge Calculations

[Kavyashree M]

Sir,

This g_hbond will generate a matrix similar to
what g_saltbr would have given in terms of variation
of distance between two charge groups.

I want to find out the variation of all the salt bridges
in the protein over the trajectory, if I have to use g_dist
with an index of positive atoms and another of negative
atoms, then it will calculate the distance between the
centre of mass of these two groups.. according to manual.

So How can I use g_dist for this kind of calculation.
I am little confused.

If I take a cut of of 0.4nm (as we mention in g_saltbr), will
it be wrong if I have to calculate salt bridges between
these two indices -

group 1: ASP_GLU_&_OD1_OD2_OE1_OE2
group 2: ARG_LYS_&_NZ_NE_NH1_NH2

Thank you
Kavya


On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/2/13 11:58 AM, Kavyashree M wrote:
>
>> Sir,
>>
>> Thank you very much for your reply. I wanted to calculate
>> Salt bridge in the whole protein so i am not mentioning the
>> residues involved. The problem with g_saltbr was that if I
>> have to calculate the accessibility of these atoms it will be
>> a problem because it gives the charge groups but not exact
>> atoms.
>>
>> This is the reason I thought of using g_hbond. But I wanted
>> clarification from experts in using this method.
>>
>> So Is there any problem if I use g_hbond?
>>
>>
> Does this really give you any useful information?  You'll get an output
> file with putative contacts derived from an arbitrary cutoff for any
> possible positive-negative pair defined in the index group.  I think the
> g_dist approach is far more useful and gives you exact insight into
> specific pairs.  It takes a bit more prep work, but looping the
> calculations is trivial to do to make them efficient.
>
> -Justin
>
>
>  Thank you
>> kavya
>>
>>
>>
>> On Tue, Apr 2, 2013 at 9:03 PM, bipin singh <bipinelmat at gmail.com> wrote:
>>
>>  You can use g_dist with specific atoms indices to calculate distances,
>>> if you already have the information about atoms involved in salt
>>> bridge interactions.
>>>
>>> On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>>>
>>>> Dear users,
>>>>
>>>> Kindly clarify my doubt regarding salt bridge calculation.
>>>>
>>>> Thank you
>>>> Regards
>>>> Kavya
>>>>
>>>>
>>>> On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>>>>
>>>>  Dear users,
>>>>>
>>>>> For calculating salt bridge in proteins I
>>>>> am using g_hbond instead of g_saltbr.
>>>>>
>>>>> In g_hbond I use contact and mention two
>>>>> indices consisting of
>>>>> group 1: ASP_GLU_&_OD1_OD2_OE1_OE2:
>>>>> group 2: ARG_LYS_&_NZ_NE_NH1_NH2:
>>>>>
>>>>> I use the command:
>>>>> g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm
>>>>> matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 50000
>>>>>
>>>>> Is this approach correct?
>>>>>
>>>>> Thank you
>>>>> Kavya
>>>>>
>>>>>  --
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>>> --
>>> -----------------------
>>> Thanks and Regards,
>>> Bipin Singh
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> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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