Re: [AMBER] Clarification on forming covalent linkages

From: David A Case <>
Date: Fri, 1 Jun 2018 08:26:00 -0400

On Fri, Jun 01, 2018, senal dinuka wrote:

> I use AMBER16 with AMBER17 Tools to model the protein 1gos. Literature says
> that the protein contains an FAD molecule connected to the protein via
> covalent bond to the 394 cysteine residue.
> I have generated parameters for FAD separately via parmchk and have used
> tleap to combine the two.
> I then used the bond command to connect the Sulfur gamma atom and the
> corresponding atom on the protein. How do I find out if this has occurred
> correctly?

ParmEd is generally the simplest way to examine a prmtop file: use the
printBonds command for your example.

...good luck....dac

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Received on Fri Jun 01 2018 - 05:30:03 PDT
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