VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Jun 03 2019 - 23:32:30 CDT

Dear everyone,

I am learning the tutorial of preparing MD simulation input files of protein-ligand complex with amber at http://ambermd.org/tutorials/pengfei/index.htm. It begins with the structure 1ODX and at the end "1ODX.prmtop" and "1ODX.inpcrd" cat be obtained for simulation.

I wish to see the structure in VMD. However, after loading the "1ODX.prmtop" and "1ODX.inpcrd" file into VMD, I find they are shown improperly. The water molecules become trianges and some protein atoms extent far away from the protein position and form llong lines.

Please find the "1ODX.prmtop" and "1ODX.inpcrd" files and the snapshot of the vmd OpenGL Display respectivelt at:
 (https://drive.google.com/open?id=1NaUCT0FtTi7zHTQjMqzs4OXWC70F08QY);
 (https://drive.google.com/open?id=1mSAXXCYHlzZ3kmV4DxplXPIVK9HQ2lb1)
(https://drive.google.com/open?id=1VEjZfGasN6uzVWbjDl6qNXapb5WlyPK8)

Is there any trick of visulization of structure in amber coordinate format? Could you help me with this?

Thank you in advance

Arthur