[gmx-users] Re: g_saltbr

[Ilya Chorny]

The code would not know that *a priori*. This list is generated before the
frames are analyzed.

Thanks,

Ilya


On Tue, Jul 27, 2010 at 12:40 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Ilya Chorny wrote:
>
>> I have a question about the g_saltbr output. I looked through the mailing
>> list and could not find a suitable answer.
>> The initial output lists all the charge group i.e.
>>
>> CG:      ARG24 Q:   0.07  Atoms:   58   59   60
>> CG:      ARG24 Q:   0.31  Atoms:   61   62   63
>> CG:      ARG24 Q:   0.38  Atoms:   64   65   66
>> CG:      ARG24 Q:   0.12  Atoms:   67   68   69
>> CG:      ARG24 Q:   0.12  Atoms:   70   71   72
>> CG:      ASP28 Q:   -0.1  Atoms:   79   80   81
>> CG:      ASP28 Q:   -0.9  Atoms:   82   83   84
>> CG:      ARG36 Q:   0.07  Atoms:   94   95   96
>> CG:      ARG39 Q:   0.31  Atoms:   97   98   99
>> CG:      ARG42 Q:   0.38  Atoms:  100  101  102
>> CG:      ARG45 Q:   0.12  Atoms:  103  104  105
>> CG:      ARG48 Q:   0.12  Atoms:  106  107  108
>> CG:      ARG60 Q:   0.07  Atoms:  118  119  120
>> CG:      ARG63 Q:   0.31  Atoms:  121  122  123
>>
>> In some cases it lists 4 charge groups for ARG (i.e. ARG24) and in others
>> it list 1 charge group (i.e. ARG 36). Why is this?
>>
>>
> Perhaps because not all the charge groups of Arg36 are participating in
> salt bridges, whereas in Arg24 they are.
>
> -Justin
>
>
>  Thanks,
>>
>> Ilya
>>
>>
>>
>> --
>> Ilya Chorny Ph.D.
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



-- 
Ilya Chorny Ph.D.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100727/9f8aa27c/attachment.html>