[gmx-users] Re: g_saltbr

[Ilya Chorny]

I have not looked at the source but I believe g_saltbr looks through the
topology and lists all possible charge groups. It then analyzes the
trajectory and outputs interactions between charge groups within the cutoff.
The default cuttoff is 1000 nm so every charge group interaction should be
accounted for.

Now that being said, I think I found the bug. I created a subset trajectory
and tpr file that only included the ARG,LYS,APS,GLU residues. When I run
g_saltbr on the trajectories containing all the residues this bug goes
away.

Ilya


On Tue, Jul 27, 2010 at 1:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Ilya Chorny wrote:
>
>> The code would not know that /a priori/. This list is generated before the
>> frames are analyzed.
>>
>>
> I'm not implying that the code is going to pre-judge your system.  If what
> you've shown is your output, wouldn't it make sense that g_saltbr only
> prints out the information for groups actually participating in putative
> salt bridges?  Otherwise, the tool will print all charge groups and render
> itself useless. Do you for some reason expect the quoted arginines to be
> equivalent?
>
> -Justin
>
>  Thanks,
>>
>> Ilya
>>
>>
>> On Tue, Jul 27, 2010 at 12:40 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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 <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
>>
>>
>> --
>> 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
>
> ========================================
> --
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-- 
Ilya Chorny Ph.D.
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