[AMBER] Visualization of all-in-one mdcrd file in VMD

From: Trang Nguyen <trangnt.iastate.edu>
Date: Tue, 10 May 2016 13:26:02 -0500

Hi All,

I have trouble when visualizing mdcrd trajectory in VMD 1.9.2. I have
searched the problem first but still cannot solve it.

I would like to generate one mdcrd file (only complex of protein-ligand,
increase time step to reduce size) from multiple mdcrd files from
simulation. What I have tried

parm com-sol.prmtop
trajin md1.mdcrd 1 500 50
trajin md2.mdcrd 1 500 50
strip :WAT,Na+
trajout md-all.mdcrd
trajout md-all.pdb

md-all.pdb is normally visualized with VMD. But mdcrd file cannot. (Bonds
are distorted). I tried with com-sol.prmtop, md-all.mdcrd (Amber coordinate
with and without periodic box). I also make new prmtop without box
information and WAT, but still not working.

Could you please suggest me any idea to solve this problem.

Thanks in advance.
AMBER mailing list
Received on Tue May 10 2016 - 11:30:03 PDT
Custom Search