AMBER Archive (2009)

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

From: case (case_at_biomaps.rutgers.edu)
Date: Sun Nov 29 2009 - 19:41:24 CST

On Mon, Nov 30, 2009, cyk5056 wrote:

> 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?

Note that "cannot open file" may not have anything to do with netcdf; are you
sure the file is there and readable?

As best I can tell, the "standalone" ptraj comes shipped with pre-compiled
netcdf for ELF (Linux) x86_64. If you have this type of system, you should be
in good shape, but I don't see any simple way to use ptraj-9.9i.tar.gz to
compile for a different architecture (I may we be missing something here).

The recommended (by me!) way to get ptraj is to download and install
AmberTools from http://ambermd.org. After configuring, you can just cd to the
ptraj directory and type "make install" if you really don't want to compile
anything else. But it is really quite simple to install the entire package.

...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber