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
