- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Jag Silwal <jagsilwal.gmail.com>

Date: Fri, 19 Jan 2018 13:23:06 -0500

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

Received on Fri Jan 19 2018 - 10:30:02 PST

Date: Fri, 19 Jan 2018 13:23:06 -0500

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

Received on Fri Jan 19 2018 - 10:30:02 PST

Custom Search