[gmx-users] Regarding calculation of Salt bridge between specific group of atoms

[bipin singh]

Thanks Sir,
I understood..

On Sat, Jun 11, 2011 at 17:30, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> bipin singh wrote:
>>
>> Dear all,
>>
>> I want to calculate the salt bridge interaction between a particular
>> set of residues,
>> because I can not use index file with g_saltbr, so the next options
>> available are
>> g_dist and g_mindist. As stated in manual g_dist gives the  distance
>> between the
>> center of mass of two groups of atom, while g_mindist gives us the minimum
>> distance between any pair of atom.
>> My doubt is that which distance(either given by g_dist or g_mindist)
>> corresponds to the salt bridge interaction distance
>> between two atoms.
>
> Not necessarily either.  g_dist measures COM distances between the given
> index groups, and g_mindist measures the minimum distance of any atom pair,
> which, for a multi-atom index group, may change over time.
>
> The solution is to create specific index groups.  If you want the distance
> between two specific atoms, create two index groups of one atom each and use
> g_dist (or g_mindist, because in this case the output would be identical).
>  If you want the distance between, e.g. the amino group of lysine and the
> carboxylate of glutamate, then the amine group with have four atoms (NZ,
> HZ1, HZ2, HZ3) and the carboxylate group will have 3 (CD, OE1, OE2).  Then
> use g_dist.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
-----------------------
Regards,
Bipin Singh