Re: [AMBER] Modified cysteine parameters

From: David A Case <>
Date: Sun, 19 Jul 2020 07:43:13 -0400

On Sun, Jul 19, 2020, krishnendu sinha wrote:

>I was trying to generate parameters for modified cysteine residue (cysteine
>geranyl) In my protein it is the C terminal residue. For generating the
>parameter I have followed the B5 tutorial ( Green Fluorescent Protein). I
>am attaching all the necessary file. WT.pdb the pdb file after running
>pdb4amber. CGR is the name of the modified residue.

It would help if you summarized the error message in the text of your email.
Here is the key line:

  Created a new atom named: OXT within residue: .R<CGR 190>

You have an OXT atom in the WT.pdb file for residue 190, but there is no
correponding OXT atom in the prepin file you created. In fact, the prepin
file as a bond to the "+M" atom (the next mainchain atom in the chain),
indicating that it is set up for a internal residue, not a C-terminal one.

I'd suggest starting from the CCYS residue, and generating your changes from
that; this should give you a C-terminal modified cysteine.

...good luck...dac

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Received on Sun Jul 19 2020 - 05:00:03 PDT
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