Re: [AMBER] ptraj rms error

From: Beale, John <>
Date: Thu, 17 Jun 2010 06:30:58 -0500

Hi Dan,

I didn't tell you - the pdb file of the x-ray structure loads perfectly
in Chimera and VMD.


-----Original Message-----
From: Daniel Roe []
Sent: Wednesday, June 16, 2010 2:54 PM
To: AMBER Mailing List
Subject: Re: [AMBER] ptraj rms error

On Wed, Jun 16, 2010 at 11:30 AM, Beale, John <>
> The "readAmberRestart" error message would seem to indicate that the
> program is looking for a restart file. I thought that ptraj would use
> pdb file as input to the reference command.

Exactly. This indicates that Ptraj did not identify str.pdb as a pdb
file for some reason. Does this file load up correctly in other
programs? How was it generated?


Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854
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Received on Thu Jun 17 2010 - 05:00:03 PDT
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