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

From: David A Case <>
Date: Wed, 29 Sep 2021 08:47:47 -0400

On Wed, Sep 29, 2021, wrote:

> 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.

I think you want the CHARMM-GUI to make the entire system, including water
and ions, before creating Amber-compatible files. Amber won't know about
residues like DIP, so (generally speaking) you want to use the parm7 file
that CHARMM-GUI creates, not try to modify it. [Small edits to parm7 files
can be made with ParmEd, but it is not set up to do major surgery.]

...good luck...dac

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Received on Wed Sep 29 2021 - 06:00:02 PDT
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