From: JC Gumbart (
Date: Wed Dec 10 2008 - 16:16:25 CST

The pdbalias lines are independent of the protein you're using.
Regarding the coordinate file, make sure you are in the proper
directory that the file is located in. If you type "ls" (in Unix/Mac/
tkcon) or "dir" (in windows) and don't see the name of the coordinate
file, then you are in the wrong place.

On Dec 10, 2008, at 11:32 AM, gurunath katagi wrote:

> respected sir,
> in your tutorial, page no.9 , u have given the script for creating
> psf file
> in line no. 6.... for reading coor file...
> if it for protein other than ubq that u have given... its giving
> cannot read the coor file...
> what may be the reason..
> how do we know the pdb alias of different aotms or residues
> thank u
> Gurunath
> IISC ,Bangalore

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