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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
*

*>> AMBER.ambermd.org
*

*>> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

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:

-- ------------------------- 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 AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jan 19 2018 - 15:00:02 PST

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