Sorry, I have found the problem myself.... Seems that my trajectory is netcdf format so I have to use the latest version online.
I downloaded the ptraj-9.9i.tar.gz online and install it by simply running "make" after unzipping the file. However, I do not know how to install the netcdf part of the packet. So it still cannot read my trajectory. Do you have any suggestions about how to install netcdf of ptraj?
Thank you!
cyk5056
2009-11-30
发件人： cyk5056
发送时间： 2009-11-30 06:06:50
收件人： amber
抄送：
主题： How to compile and recompile ptraj?
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
http://www.chpc.utah.edu/~cheatham/software.html.
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 bbproteinptraj.in" 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!
cyk5056
2009-11-30
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Received on Sun Nov 29 2009 - 15:00:02 PST
