[AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system

From: <neildancer.sina.com>
Date: Wed, 29 Sep 2021 11:47:14 +0800

Hi Amber expert,
  Recently, I need a suitable system to simulate the progress about protein binding with the glycolipid molecule. I had used the CHARMM-GUI web server to generate the parm7 and pdb files of MGDG, which was the key component of thylakoid membrane of chloroplast. But, I don't know how to combine this parm7 file of MGDG into the big simulation system that containing protein, water and salt molecules. I had tried to use the tleap program to generate the MGDG's OFF file, and to reload it with "loadoff" command. However, it didn't work, tleap reminded me some errors like that "FATAL: Atom .R<DIP 342>.A<C37 76> does not have a type". Please help me. Any suggestions are welcome.
Best regards,

Ning Wang <PhD>
National Laboratory of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences

My reseached interests has foucsed on protein structure determinated by Cryo-EM, virtual screening of potential drugs, protein molecular dynamic simulation, and protein design via computational biology.

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Received on Tue Sep 28 2021 - 21:00:03 PDT
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