Re: [AMBER] Preparation of i-Motif structures

From: David A Case <>
Date: Tue, 22 Jun 2021 15:58:54 -0400

On Wed, Jun 23, 2021, Sruthi Sudhakar wrote:
>I tried to fix the column error and try to reload it, still the structure
>in both leap as well as in the visualization tools shows error. I am
>attaching the pdb here. Other than manually editing the pdb text file, is
>there a way to change the residue names?

You pdb file is still mal-formed: You have ATOM lines that look like this:

ATOM 1 O5' D5C A 1 7.765 7.447 7.155 1.00 0.00 O

But they should look like this: (copied from one of my PDB files)

ATOM 2 O5' G5 1 47.705 51.648 49.371 1.00 0.00 O

Everything after about column 23 is shifted one column to the right. Make
sure you can visualize your structure in a program like VMD or Chimera
before trying to continue.

A text editor is probably the best choice to change residue names.

...good luck....dac

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Received on Tue Jun 22 2021 - 13:00:03 PDT
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