AMBER Archive (2002)

Subject: plep question

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Jun 26 2002 - 02:28:23 CDT

Dear Amber-users,

I am learning how to use 'prep/link/edit and parm'. Although I know it is
now replaced by 'leap' I would like to use 'plep'. I loaded my unit (unusual
residue, MOL) and generated a 'prep_mol.in' file using the 'leap' command
'saveamberprep' (Cartesian coordinates format). Then, I ran 'prep' saving
the ouput in a binary file MOL.res (not in the database).
- As this unusual unit is the unique component of my molecule I want to work
on, should I run 'link' or can I use this binary 'prep' file directly with
'edit' ?

Moreover, I tried different inputs for 'link' (in case I have to use 'link')
without success. As I said, the 'prep' output of this unusual residue is
saved in a MOL.res file and not in the database. When I run 'link' the
database is loaded with the option '-p'.
- Should I save the 'prep' output in the database before running 'link' or
can I use it as a unique file (i.e. without loading the database) ?

Thanks a lot, Kind regards, Francois