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From: giulia palermo <giulia.palermo83.gmail.com>

Date: Thu, 13 Nov 2014 12:44:52 +0100

Dear Daniel,

thank you for your suggestions. I also have an other question.

Is there a direct way with ptraj or cpptraj to calculate the angle 'tau'

between the principal axis of an alpha-helix and the z-axis of my reference

system (i.e. the cartesian coordinates)??

Moreover, after having calculate the 'tau' angle for an alpha-helix, is it

possible to directly calculate with ptraj/cpptraj the time correlation

function between this angle and the 'tau' angle of an pther alpha-helix??

I have a complex system in which I need to understand how the movements of

one alpha-helix is correlated in time with the movement of an other

alpha-helix. Thus, I thought that the angle between the pricipal axis of

the helices and the z-reference axis could be a suitable metrix.

I also wonder if there are other commands in ptraj that allow to calculate

the helix-tilting that could be an other suitable metrix for solving my

probelm.

Thank you very much

Best regards.

2014-11-12 19:37 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:

*> Hi,
*

*>
*

*> On Wed, Nov 12, 2014 at 11:04 AM, giulia palermo
*

*> <giulia.palermo83.gmail.com> wrote:
*

*> > I assume that the principal axis is stored in the second column (0.7802,
*

*> > 0.8411, 0.6899 ...).
*

*> > Could you please clarify this point?
*

*>
*

*> As stated at the top of the vector output file the vector is stored as
*

*> "vx vy vz cx cy cz cx+vx cy+vy cz+vz", so the X Y and Z components of
*

*> the principal axis (i.e. the axis with the largest eigenvalue) for
*

*> each frame are in the second, third, and 4th columns respectively. The
*

*> next 3 columns are the X Y and Z coords of the center of mass of the
*

*> atoms in the mask, and the final 3 columns are the sums of each
*

*> component.
*

*>
*

*> > Moreover, if I subsequently specify the following command in order to
*

*> > obtain the time-correlation between v0 and v1, I do not obtain any
*

*> output.
*

*> >
*

*> > analyze timecorr vec1 v0 vec2 v1 tstep 1.0 tcorr 10000.0 out v0_v1.out
*

*>
*

*> I think that 'timecorr' from ptraj can only use vectors that are
*

*> marked with the 'corr' keyword. You should use cpptraj instead, which
*

*> doesn't have this restriction.
*

*>
*

*> -Dan
*

*>
*

*> PS - The 'timecorr' analysis command calculates autocorrelations using
*

*> spherical harmonic averaging, so make sure that's what you want to do.
*

*>
*

*> >
*

*> > Do you have any suggestions that can help me in doing this analysis?
*

*> >
*

*> > Thank you
*

*> > Best regards
*

*> >
*

*> > Giulia
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

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

*>
*

*>
*

*>
*

*> --
*

*> -------------------------
*

*> Daniel R. Roe, PhD
*

*> Department of Medicinal Chemistry
*

*> University of Utah
*

*> 30 South 2000 East, Room 307
*

*> Salt Lake City, UT 84112-5820
*

*> http://home.chpc.utah.edu/~cheatham/
*

*> (801) 587-9652
*

*> (801) 585-6208 (Fax)
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

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Received on Thu Nov 13 2014 - 04:00:06 PST

Date: Thu, 13 Nov 2014 12:44:52 +0100

Dear Daniel,

thank you for your suggestions. I also have an other question.

Is there a direct way with ptraj or cpptraj to calculate the angle 'tau'

between the principal axis of an alpha-helix and the z-axis of my reference

system (i.e. the cartesian coordinates)??

Moreover, after having calculate the 'tau' angle for an alpha-helix, is it

possible to directly calculate with ptraj/cpptraj the time correlation

function between this angle and the 'tau' angle of an pther alpha-helix??

I have a complex system in which I need to understand how the movements of

one alpha-helix is correlated in time with the movement of an other

alpha-helix. Thus, I thought that the angle between the pricipal axis of

the helices and the z-reference axis could be a suitable metrix.

I also wonder if there are other commands in ptraj that allow to calculate

the helix-tilting that could be an other suitable metrix for solving my

probelm.

Thank you very much

Best regards.

2014-11-12 19:37 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:

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Received on Thu Nov 13 2014 - 04:00:06 PST

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