[gmx-users] why the output of g_saltbr is so large?

[francesco oteri]

You should modify g_saltbr code.
Alternativley, you can create a fake .top file where charge are 0 except on
carged groups (i.e. carboxylic atoms) that are supposed to interact.
This new .top file can be used to have a new .tpr where only the
interesting atoms
are charged and are detected by g_saltbr as part of a putative interaction.

Francesco

2012/9/21 Albert <mailmd2011 at gmail.com>

> On 09/21/2012 10:48 AM, francesco oteri wrote:
>
>> Hi,
>> because g_saltbr calculates the data regarding any charge-charge
>> interaction ( neg neg, neg pos, pos pos).
>> Small problem: every atoms (C,H,S,P...) has a charge so the outputs
>> contains the distances among al the
>> n*(n-1)/2  atom couples!!!!
>>
>> Francesco
>>
>
> Hello :
>
> thank you very much for kind reply.
> Is it possible simple restrict the calculation to protein sidechain?
>
>
> thank you very much
> best
> Albert
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-- 
Cordiali saluti, Dr.Oteri Francesco