Re: [AMBER] CPPTRAJ-Angle between two Helices

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 19 Jan 2018 17:39:24 -0500

Usually what I do is use the center of mass of backbone atoms of
residues that make up the beginning and ending repeats, something
like:

vector :1-4.C,CA,N :17-20.C,CA,N

where residues 1-4 make up one end of the helix and 17-20 make up the
other. This of course assumes the helix itself is fairly linear.

-Dan

On Fri, Jan 19, 2018 at 4:15 PM, Arati Paudyal <apsilwal123.gmail.com> wrote:
> Dan,
>
> Thanks for your email. I will give it a try. I will also try in another
> protein to verify this.
>
> But am I using the mask correctly here? Basically, I am trying to
> calculate the angle between two helices by choosing a common atom (2316)
> from the loop region that connects two helices. Is this how its commonly
> done? I just wanted to make sure I am correct on this one before I do other
> calculations.
>
> Thank you again!!
>
>
> Sincerely,
> Jag
>
> On Fri, Jan 19, 2018 at 3:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Tough to really say what might be going on here without seeing the
>> system. One thing I like to do in these situations is actually
>> visualize the vectors themselves. You can do this by writing the
>> vector data out in 'vectraj' (vector pseudo-trajectory) format, like
>> so:
>>
>> vector Helix1 .2018 @2316
>> vector Helix2 .2316 @22841
>> run
>> writedata vectors.nc vectraj Helix1 Helix2 trajfmt netcdf parmout
>> vectors.parm7
>>
>> Then you can visualize what the 'vector' commands are actually
>> calculating and see if those are good representations of your helices.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Fri, Jan 19, 2018 at 1:23 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
>> > Dear all,
>> > I want to measure the angle between two helices in a protein for the
>> > entire simulation (angle Vs time). I found the following guide from Dan
>> and
>> > I followed it and ran a sample run for one of the helices. I got the
>> > results and everything but the angle is almost double what I was
>> expecting
>> > for the entire run.
>> > So, I think I mightn't be using 'atom mask' properly here. So the two
>> > helices are connected by a small loop with the turn of about 50 degrees.
>> If
>> > the starting of one helix is residue 'A' then turns at residue 'B' and
>> > continues as another helix which ends at residue 'C', can I use the mask
>> as
>> > follows:
>> > vector Helix1 .2018 @2316
>> > vector Helix2 .2316 @22841
>> > Where, *the numbers are the C-alpha atom number for residues A, B and C.*
>> >
>> > Did I do this right?
>> >
>> > Any insight would be helpful.
>> >
>> > Sincerely,
>> > Jag
>> > ............................................................
>> ............................................................
>> ...............
>> > One thing you can try is calculating the angle between the vectors that
>> run
>> > along the helices; this can be done with cpptraj. First, read in your
>> > topology and trajectory:
>> > parm MyParm.parm7
>> > trajin MyTraj.nc <https://www.researchgate.net/
>> deref/http%3A%2F%2FMyTraj.nc>
>> > Then you would create the vectors:
>> > vector Helix1 <mask1> <mask2>
>> > vector Helix2 <mask3> <mask4>
>> > Here, mask1 and mask2 are atom masks defining each end of the first helix
>> > and mask3 and mask4 are atom masks defining each end of the second helix.
>> > Then you can use the 'vectormath' analysis command to calculate the angle
>> > between the vectors:
>> > vectormath vec1 Helix1 vec2 Helix2 dotangle out H1-H2-angle.dat
>> > Hope this helps,
>> > -Dan
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>> _______________________________________________
>> AMBER mailing list
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>>
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-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Jan 19 2018 - 15:00:02 PST
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