[gmx-users] Re: Salt bridge Calculations

[bipin singh]

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