AMBER Archive (2009)

Subject: Re: [AMBER] prep file

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Sep 04 2009 - 09:09:06 CDT

On Fri, Sep 04, 2009, Jio M wrote:
>
> I have used small residues made under gaff and joined them to make
> large macromolecule taking  care of atom types after joining...
> all small residues were saved as mol2 then saved in .lib file.By using
> the library having small residues I made macromolecule and also saved
> macromolecule (named abc) in .lib file
>
> to make prmtop and inpcrd file I used following:
> source leaprc.gaff
> loadoff mylibrary.lib
> saveamberparm abc abc.prmtop abc.inpcrd
>
> But I have seen many people using "prep" file to make prmtop and
> inpcrd. can we not use directly our molecule saved in .lib library as I
> have done or also we can use mol2 file
>
> what is advantage of using prep file?

There is no advantage to the prep file, and we are hoping to eventually retire
that file format. Its use is historical, but there are lots of existing prep
files, so we will continue to support them. Making mol2 files is probably the
best idea, since they are widely recognized (say by visualization programs),
they are pretty self-documenting, and they contain all the necessary
information. Using .lib files is OK, but only Amber programs recognize that
format.

...dac

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