Re: [AMBER] puckering coordinates

From: Pratul Agarwal <pratul.agarwal-lab.org>
Date: Tue, 19 Feb 2019 18:19:18 +0000

Myrian,

If the numbers correspond to atoms in the ring of your interest, then the command you perhaps need is:
>pucker p1 .2175 .2191 .2187 .2185 .2178 .2177 out pucker.dat cremer amplitude theta range360

Pratul


Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/


On 2/19/2019 11:25 AM, MYRIAN TORRES RICO wrote:

Hi Mish,

Thanx for your answer.
My script is this:

trajin /home/cristina/smp-196ptn/md125ns/ptn4rig_vcon.mdcrd
pucker p1 :2175 :2191 :2187 :2185 :2178 :2177 out pucker.dat cremer
amplitude theta range360

and I obtain one only measure (phi maybe)...


#Frame p1
        1 2431.7465
        2 2413.8681
        3 2491.5866
        4 2580.4869
        5 2335.1242
        6 2714.6331
.
.
.

why?

thanx in advantage

Myriam


mish <smncbr.gmail.com><mailto:smncbr.gmail.com> escribió:



If you are using Glycam force-filed, ring atoms are named as C1, C2, C3,
C4, C5 and O5. Following command in *cpptraj* will give you angle,
amplitude and theta:



pucker d1 :4.C1 :4.C2 :4.C3 :4.C4 :4.C5 :4.O5 out puckering.dat cremer


amplitude theta range360

analyz$ head -4 puckering.dat
#Frame d1 d1[Amp] d1[Theta]
       1 112.9888 0.5533 170.4752
       2 27.2829 0.5627 164.2702
       3 95.4169 0.6143 172.6282

all the best.

On Tue, Feb 19, 2019 at 1:52 PM Pratul Agarwal <pratul.agarwal-lab.org><mailto:pratul.agarwal-lab.org>
wrote:



Hi Myriam,

Has anyone replied to your query? I didn't see any response.

Have you tried using cpptraj? The command will be:


pucker p1 :1.C1’ :1.C2’ :1.C3’ :1.C4’ :1.O4’ range360 out pucker.dat



See the manual for further details.

Pratul

Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/


On 2/18/2019 12:54 PM, MYRIAN TORRES RICO wrote:

Hi all,

I have a complex protein-saccharide and I want to calculate the
puckering coordinates (q,f) in the six ring. How is the scrypt?

thanx in advantage

Myriam


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Received on Tue Feb 19 2019 - 10:30:05 PST
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