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

francesco oteri francesco.oteri at gmail.com
Fri Sep 21 11:49:24 CEST 2012

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.


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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>

Cordiali saluti, Dr.Oteri Francesco

More information about the gromacs.org_gmx-users mailing list