AMBER Archive (2009)

Subject: RE: [AMBER] bintraj and amber 10

From: Ross Walker (
Date: Wed Apr 22 2009 - 05:59:47 CDT

Dear Naser

> I am try the following command in Amber 10: ./configure_amber -bintraj
> -openmpi ifort
> unknown flag -bintraj

There is no -bintraj flag for AMBER 10 configure_amber anymore. Unlike
Amber9 bintraj support is now the default so you just have the option to
turn it off using the flag '-nobintraj'.

Note, this is different to PMEMD compilation where you have to explicitly
request bintraj support by specifying -bintraj.

> ./configre_amber -help are "-nobintraj" (so I just tried IOUTFM=1 and
> there
> was no error but ptraj does not recognize the format so there is a
> problem).

Did you build ptraj (as part of amber tools ./configure_at) with netcdf
support? This should be the default but there may have been problems during
the build process or you are using an old version of ptraj without realizing
it. Also make sure you have applied bugfix.3 for your AmberTools

Programs: ptraj

Description: Fixes multiple problems.
             1) Ptraj did not correctly open netcdf files.
             2) Ptraj misidentified Amber REMD restarts as trajectories.
             3) io.c contained duplicate code in openFile() that resulted
                in strange behavior for bzipped files.
             4) gzipped amber remd trajectories are now handled correctly.
             5) remd trajectories can now have numerical extensions of
                arbitrary width, not just %03i.
             6) Better error checking and more informative error messages
                for remd traj code.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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