AMBER Archive (2007)

Subject: RE: AMBER: is not normal

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Aug 20 2007 - 21:51:16 CDT

Hi Qiang,

> below information ,it is not like tutorial .
> [t_at_localhost ~]$ tleap
...
> Welcome to LEaP!
> (no leaprc in search path)

> in tutorial file, normal result should be:
>
> Sourcing leaprc: /amber/dat/leap/cmd/leaprc
...
>

Which tutorial is this you are refering to? This is ancient behavior and the
tutorial is really in need of updating. Leap no longer has a default force
field since this is of little use given the diversity that now exists in
force fields. If this is one of the tutorials on the Amber website then let
me know and I'll update it... If it is another tutorial somewhere then you
should probably contact the author and ask them to update the tutorial or
provide a link to the more up to date tutorials on the Amber website.

You will need to work out what force field the tutorial expects you to be
using by default. (ala Amber 6). Probably it is FF94 in which case you need
to issue the command

source leaprc.ff94

Although I would not recommend using this for "real" simulations. A more
appropriate option is probably FF99SB or FF03.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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