Re: [AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file

From: Daniel Roe <>
Date: Thu, 1 Dec 2011 16:10:29 -0500


I'm unable to reproduce the error you see with ptraj from AmberTools
1.2 or 1.5. What does the 'Version' string printed at the beginning of
ptraj output say? (For example, in AmberTools 1.2 it should read
Version: "AMBER 10.0 integrated"). If you run 'ptraj H107Y_all.psf'
you should see something like:

  \-/ Reading in CHARMM PSF file
Reading in the title...

 REMARKS original generated structure x-plor psf file
Dumping state information...
  atoms: 46844
  residues: 14517

On Wed, Nov 30, 2011 at 12:08 AM, Puspita Halder <> wrote:
> I have another question for you. You mentioned in your last e-mail about
> the website for AmberTools with all bug-fixes applied. As I already
> mentioned that we have the amber 9 package installed in our lab. So with
> this can I use the above mentioned ambertools?

You can use AmberTools 1.5 alongside Amber9. AmberTools 1.5 will
unpack into a separate amber11 directory. Just make sure you are
setting AMBERHOME to point towards the AmberTools 1.5 install.


Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ   08854
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Received on Thu Dec 01 2011 - 13:30:02 PST
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