Re: [gmx-users] Salt bridge observation

[Justin Lemkul]

On 4/4/13 5:18 AM, Kavyashree M wrote:

Ok. Still the distance is beyond the mentioned
cut-off. The distance of both OD1 and OD2 of
ASP is more than 4 Ang from NH2 of Arg.



The cutoff is applied per group, not per atom within the group, IIRC.  So if the 
charge group at any time comes closer than 0.4 nm, you get an output file for it.


-Justin

--


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] Salt bridge observation

[Kavyashree M]

Ok. Still the distance is beyond the mentioned
cut-off. The distance of both OD1 and OD2 of
ASP is more than 4 Ang from NH2 of Arg.

Thank you
Regards
Kavya


On Thu, Apr 4, 2013 at 2:25 PM, Justin Lemkul  wrote:

>
>
> On 4/4/13 4:34 AM, Kavyashree M wrote:
>
>> Sir,
>>
>> Why I mentioned NH2 CG saltbridge because the g_saltbr
>> gives the charge group and does not mention the OD2 of ASP
>> but mentions only CG. Otherwise it does not make any sense.
>>
>>
> Now I remember how g_saltbr naming works.  It measured distances between
> charge groups, and the file names are based on the first atom in the charge
> group, so "CG" indicates the gamma-carboxylate group of ASP, which includes
> both OD1 and OD2.
>
>
> -Justin
>
> --
> ==**==
>
> 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] Salt bridge observation

[Justin Lemkul]

On 4/4/13 4:34 AM, Kavyashree M wrote:

Sir,
Why I mentioned NH2 CG saltbridge because the g_saltbr
gives the charge group and does not mention the OD2 of ASP
but mentions only CG. Otherwise it does not make any sense.



Now I remember how g_saltbr naming works.  It measured distances between charge 
groups, and the file names are based on the first atom in the charge group, so 
"CG" indicates the gamma-carboxylate group of ASP, which includes both OD1 and OD2.


-Justin

--


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] Salt bridge observation

[Kavyashree M]

Sir,
Why I mentioned NH2 CG saltbridge because the g_saltbr
gives the charge group and does not mention the OD2 of ASP
but mentions only CG. Otherwise it does not make any sense.

Thanks
Regards
Kavya


On Thu, Apr 4, 2013 at 1:53 PM, Justin Lemkul  wrote:

>
>
> On 4/4/13 12:27 AM, Kavyashree M wrote:
>
>> Sir,
>>
>> That is true, previously you had explained regarding this.
>>
>> Calculation using g_saltbr
>> 1. For g_saltbr I included the following residues -
>>  ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
>>  which contained only these residues. sb was calculated using -
>>
>> g_saltbr -f traj.xtc  -s md.tpr  -b 4000 -e 4000 -t 0.4 -sep
>>
>> 2. Files that were generated were filtered and only those having
>>  sb between ASP, GLU and ARG LYS were retained.
>>
>> 3. Further, out of these sbs, those which had the following atoms
>>  CG  ASP, CD  GLU, NE  ARG, NH1 ARG, NH2 ARG, NZ  LYS
>>  were retained.
>>
>> Calculation using g_hbond -
>> It was done using the index file mentioned in my previous post using
>>
>> g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm
>> -hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000
>>
>> So essentially the final results in both are composed of sbs formed
>> between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr
>> while charged atoms in case of g_hbond.
>>
>> The comparison showed that all sbs from g_hbond were present
>> in the output from g_saltbr. But g_saltbr had some additional sbs
>> off-course between the same charged groups. But only the distance
>> was greater than 4 Ang for ex-
>> distance between NH2 ARG and OD2 ASP is 4.32Ang
>> Since it considers charged group CG of ASP instead of OD2 ASP
>> distance between NH2 ARG and CG ASP is 5.54 Ang
>>
>>
> So g_saltbr is doing something weird, though I don't see how it is
> possible to be honest.  It's up to you to filter the information by what
> you believe to be useful.  An NH2-CG salt bridge likely doesn't make any
> sense at all, anyway.
>
>
> -Justin
>
> --
> ==**==
>
> 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] Salt bridge observation

[Justin Lemkul]

On 4/4/13 12:27 AM, Kavyashree M wrote:

Sir,

That is true, previously you had explained regarding this.

Calculation using g_saltbr
1. For g_saltbr I included the following residues -
 ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
 which contained only these residues. sb was calculated using -

g_saltbr -f traj.xtc  -s md.tpr  -b 4000 -e 4000 -t 0.4 -sep

2. Files that were generated were filtered and only those having
 sb between ASP, GLU and ARG LYS were retained.

3. Further, out of these sbs, those which had the following atoms
 CG  ASP, CD  GLU, NE  ARG, NH1 ARG, NH2 ARG, NZ  LYS
 were retained.

Calculation using g_hbond -
It was done using the index file mentioned in my previous post using

g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm
-hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000

So essentially the final results in both are composed of sbs formed
between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr
while charged atoms in case of g_hbond.

The comparison showed that all sbs from g_hbond were present
in the output from g_saltbr. But g_saltbr had some additional sbs
off-course between the same charged groups. But only the distance
was greater than 4 Ang for ex-
distance between NH2 ARG and OD2 ASP is 4.32Ang
Since it considers charged group CG of ASP instead of OD2 ASP
distance between NH2 ARG and CG ASP is 5.54 Ang



So g_saltbr is doing something weird, though I don't see how it is possible to 
be honest.  It's up to you to filter the information by what you believe to be 
useful.  An NH2-CG salt bridge likely doesn't make any sense at all, anyway.


-Justin

--


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] Salt bridge observation

[Kavyashree M]

Sir,

That is true, previously you had explained regarding this.

Calculation using g_saltbr
1. For g_saltbr I included the following residues -
ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
which contained only these residues. sb was calculated using -

   g_saltbr -f traj.xtc  -s md.tpr  -b 4000 -e 4000 -t 0.4 -sep

2. Files that were generated were filtered and only those having
sb between ASP, GLU and ARG LYS were retained.

3. Further, out of these sbs, those which had the following atoms
CG  ASP, CD  GLU, NE  ARG, NH1 ARG, NH2 ARG, NZ  LYS
were retained.

Calculation using g_hbond -
It was done using the index file mentioned in my previous post using

g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm
-hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000

So essentially the final results in both are composed of sbs formed
between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr
while charged atoms in case of g_hbond.

The comparison showed that all sbs from g_hbond were present
in the output from g_saltbr. But g_saltbr had some additional sbs
off-course between the same charged groups. But only the distance
was greater than 4 Ang for ex-
distance between NH2 ARG and OD2 ASP is 4.32Ang
Since it considers charged group CG of ASP instead of OD2 ASP
distance between NH2 ARG and CG ASP is 5.54 Ang

There are some 10 more such examples. I can send the calculations
if requires.

Thank you
Regards
Kavya





On Wed, Apr 3, 2013 at 10:25 PM, Justin Lemkul  wrote:

> On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M  wrote:
>
> > Dear users,
> >
> > This is regarding an observation while calculating the
> > salt bridge (sb) using g_saltbr.
> >
> >
> > I used g_saltbr and g_hbond (with contact option) with
> > a cut of of 4Ang, for calculating sb in the whole protein
> > at a single frame.
> >
> > I made sure that I considered sb between same set of
> > residues (ASP, GLU with LYS ARG) in both calculations.
> > and filtered accordingly.
> >
> > While checking the individual sb it was found that most
> > of the results from g_saltbr matches with g_hbond but
> > g_saltbr gives some extra sbs. On checking these extra
> > sb it was found that the distance between the atoms
> > forming sb are more than the cut of I had mentioned (4 Ang).
> >
> > Not sure why it is like this. But just wanted to convey this
> > observation.
> >
> >
> Please provide a concrete example.  Note that running g_saltbr and g_hbond
> (with the index files mentioned before) should not be expected to produce
> equivalent result.  g_saltbr is relatively stupid; it considers any group
> with a charge ± 0.2 to be capable of participating in a salt bridge.  In
> some cases, this will include methylene groups or others than are near the
> actual charged groups.  Such behavior could easily account for whatever
> observation you're making.
>
> -Justin
>
> --
>
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Salt bridge observation

[Justin Lemkul]

On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M  wrote:

> Dear users,
>
> This is regarding an observation while calculating the
> salt bridge (sb) using g_saltbr.
>
>
> I used g_saltbr and g_hbond (with contact option) with
> a cut of of 4Ang, for calculating sb in the whole protein
> at a single frame.
>
> I made sure that I considered sb between same set of
> residues (ASP, GLU with LYS ARG) in both calculations.
> and filtered accordingly.
>
> While checking the individual sb it was found that most
> of the results from g_saltbr matches with g_hbond but
> g_saltbr gives some extra sbs. On checking these extra
> sb it was found that the distance between the atoms
> forming sb are more than the cut of I had mentioned (4 Ang).
>
> Not sure why it is like this. But just wanted to convey this
> observation.
>
>
Please provide a concrete example.  Note that running g_saltbr and g_hbond
(with the index files mentioned before) should not be expected to produce
equivalent result.  g_saltbr is relatively stupid; it considers any group
with a charge ± 0.2 to be capable of participating in a salt bridge.  In
some cases, this will include methylene groups or others than are near the
actual charged groups.  Such behavior could easily account for whatever
observation you're making.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Salt bridge observation

[Kavyashree M]

Dear users,

This is regarding an observation while calculating the
salt bridge (sb) using g_saltbr.


I used g_saltbr and g_hbond (with contact option) with
a cut of of 4Ang, for calculating sb in the whole protein
at a single frame.

I made sure that I considered sb between same set of
residues (ASP, GLU with LYS ARG) in both calculations.
and filtered accordingly.

While checking the individual sb it was found that most
of the results from g_saltbr matches with g_hbond but
g_saltbr gives some extra sbs. On checking these extra
sb it was found that the distance between the atoms
forming sb are more than the cut of I had mentioned (4 Ang).

Not sure why it is like this. But just wanted to convey this
observation.

Thank you
regards
Kavya
-- 
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