AMBER Archive (2004)

Subject: RE: AMBER: name error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 08 2004 - 12:35:46 CDT

Dear Prashansa,

> I am running dynamics on my system on AMBER 6 and trying to save the
> velocity, trajectory and energy files during the run. The run
> is running
> smooth but it is giving error which as /usr/bin/ccc/make -x not a
> directory ( for the trajectory file) the sme error also occurs with
> velocity and energy file as -v and -e flags.

This is a very strange error. You don't have anything weird like . Defined
in your path do you?

Try echo $PATH

How ae you running the dynamics? Are you using single processor or mpi? Also
are you definitely running the sander executable and not some strange script
that is called sander?

How about running the job without specifying any -x -e or -v flags and just
letting it use the default filenames. You can always rename them later. Do
you still get a problem?

> The files for the trajectory, velocity and energy are not saved with
> the names specified but are saved with default names as
> mdvel, mden and
> mdcrd names. I am not able to undestand why default names are
> being taken for these files

I suspect something is very messed up with your environment. What machine
type are you running this on?

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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