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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Thu, 13 Nov 2014 08:09:54 -0700

Hi,

I recommend switching to cpptraj, since it has more options and ptraj

is no longer under active development. Check out the 'ucellz' option

of the 'vector' command in cpptraj, which will store the z-axis vector

of your unit cell, as well as the 'vectormath' analysis command, which

will allow you to calculate angles between vectors.

Hope this helps,

-Dan

On Thu, Nov 13, 2014 at 4:44 AM, giulia palermo

<giulia.palermo83.gmail.com> wrote:

*> 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
*

*>>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

Date: Thu, 13 Nov 2014 08:09:54 -0700

Hi,

I recommend switching to cpptraj, since it has more options and ptraj

is no longer under active development. Check out the 'ucellz' option

of the 'vector' command in cpptraj, which will store the z-axis vector

of your unit cell, as well as the 'vectormath' analysis command, which

will allow you to calculate angles between vectors.

Hope this helps,

-Dan

On Thu, Nov 13, 2014 at 4:44 AM, giulia palermo

<giulia.palermo83.gmail.com> wrote:

-- ------------------------- 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/amberReceived on Thu Nov 13 2014 - 07:30:02 PST

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