AMBER Archive (2009)

Subject: [AMBER] How to compile and recompile ptraj?

From: cyk5056 (
Date: Sun Nov 29 2009 - 16:06:55 CST

Hi Amber users,
  I am trying to edit a little source code of ptraj. I download ptraj standalone source code ptraj-6.5.tar.Z from
  I unzip the file and enter the directory. It seems that just running "make" is OK for compiling and installation. However, after installation, I use "./ptraj bbprotein.prmtop" where .in file is:
trajin bbprotein.mdcrd
strip :WAT
rms first out rms1.txt :1-108 time .05
matrix mwcovar name bbprotein.matrix out bbprotein.matrix
analyze matrix bbprotein.matrix out bbprotein.mode vecs 400

it shows that "trajin bbprotein.mdcrd, cannot open file... ". bbprotein.mdcrd is binary trajectory file that can be read by ptraj in Amber packet.
How can I compile and install standalone ptraj correctly?

Thank you very much!

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