[gmx-users] Re: Salt bridge Calculations

[Justin Lemkul]

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

========================================