Re: [gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

[Kavyashree M]

Sir,

I used OPLS-AA ff. Thank you very mush for your effort.
Its clear now. AS you said It assigns the number of the 1st
atom of the charge group in the output file.

Thank you
kavya

On Thu, Jan 3, 2013 at 5:01 PM, Justin Lemkul  wrote:

>
>
> On 1/3/13 5:15 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> I would like to add that in case of ARG or LYS, the sidechain
>> nitrogen atoms (NE,NZ,NH1,NH2) are present in the output.
>> The problem s only with GLU and ASP residues.
>> I use 4.5.3 version
>>
>>
> I only took a quick look through the code, but it seems that what g_saltbr
> is doing is labeling its output files based on the first atom in a given
> charge group.  The charge group, not the individual atoms per se, are what
> dictate the search criteria.  You haven't said which force field you're
> using, but I will assume it's one of the Gromos ones, wherein the C[GD]
> atom is the first atom in the COO- charge group.
>
> -Justin
>
>
>  Thank you
>> kavya
>>
>> On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M  wrote:
>>
>>  Dear users,
>>>
>>> I used g_saltbr to calculate the salt-bridge interactions using:
>>> g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
>>> It gave the output for each atom-atom interaction within
>>> the given cut-off.
>>> When I checked the atom type that corresponds to the atom
>>> number output in each file, side chain oxygen atoms of ASP
>>> and GLU was not present in any of  the file. And most of the
>>> atoms that corresponds to the ASP and GLU were CB, CG or
>>> CD.
>>> Kindly someone clarify why is this so.
>>>
>>> Thank you
>>> Kavya
>>>
>>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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Re: [gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

[Justin Lemkul]

On 1/3/13 5:15 AM, Kavyashree M wrote:

Dear users,

I would like to add that in case of ARG or LYS, the sidechain
nitrogen atoms (NE,NZ,NH1,NH2) are present in the output.
The problem s only with GLU and ASP residues.
I use 4.5.3 version



I only took a quick look through the code, but it seems that what g_saltbr is 
doing is labeling its output files based on the first atom in a given charge 
group.  The charge group, not the individual atoms per se, are what dictate the 
search criteria.  You haven't said which force field you're using, but I will 
assume it's one of the Gromos ones, wherein the C[GD] atom is the first atom in 
the COO- charge group.


-Justin


Thank you
kavya

On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M  wrote:


Dear users,

I used g_saltbr to calculate the salt-bridge interactions using:
g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
It gave the output for each atom-atom interaction within
the given cut-off.
When I checked the atom type that corresponds to the atom
number output in each file, side chain oxygen atoms of ASP
and GLU was not present in any of  the file. And most of the
atoms that corresponds to the ASP and GLU were CB, CG or
CD.
Kindly someone clarify why is this so.

Thank you
Kavya



--


Justin A. Lemkul, Ph.D.
Research Scientist
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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[gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

[Kavyashree M]

Dear users,

I would like to add that in case of ARG or LYS, the sidechain
nitrogen atoms (NE,NZ,NH1,NH2) are present in the output.
The problem s only with GLU and ASP residues.
I use 4.5.3 version

Thank you
kavya

On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M  wrote:

> Dear users,
>
> I used g_saltbr to calculate the salt-bridge interactions using:
> g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
> It gave the output for each atom-atom interaction within
> the given cut-off.
> When I checked the atom type that corresponds to the atom
> number output in each file, side chain oxygen atoms of ASP
> and GLU was not present in any of  the file. And most of the
> atoms that corresponds to the ASP and GLU were CB, CG or
> CD.
> Kindly someone clarify why is this so.
>
> Thank you
> Kavya
>
-- 
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