VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Sat Apr 13 2019 - 07:34:59 CDT

Let me highly recommend Jerome Henin’s qwrap: https://github.com/jhenin/qwrap

It has easily handed so many cases that pbctools gave me weird behavior (and MUCH faster). Sometimes you have to play around with the center selection or even wrap it multiple times to get the output you want.

Best,
JC

On Apr 12, 2019, at 6:44 PM, Angana Ray <angana88ray_at_gmail.com<mailto:angana88ray_at_gmail.com>> wrote:

Hi

I am currently simulations a complex containing protein, dsDNA and RNA. The trajectory is generated in Anton2. I would like to visualize and analyze the the trajectory with VMD.

Due PBC the nucleic acid part appears to be away from the protein in VMD visualization. I want to unwrap the system such that my complex has the protein, DNA and RNA together. The pbc unwarp -sel is not working for this.

I am attaching two files here (.dms and .trr). Please let me know how this can be sorted .

Thank you
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 4un3l_init.dms<https://drive.google.com/file/d/1ky4AoaFNVa7PVbgbtU-1r2ZAb7wLelTd/view?usp=drive_web>[X]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] test.trr<https://drive.google.com/file/d/1b3Zd3lh-boL5ShzGRoGaF_IIihtXGpbt/view?usp=drive_web>[X]

regards
Angana

--
Angana Ray
Postdoctoral Scholar - Research Associate
University of Southern California
Mobile: +1-2132840728