AMBER Archive (2009)

Subject: [AMBER] prep file

From: Jio M (jiomm_at_yahoo.com)
Date: Fri Sep 04 2009 - 04:24:04 CDT

Dear Amber Users:

I have a query regarding useage of prep file..

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

I have minimised and run the dynamics though no error was there

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?

Thanks and regards:

JIomm

      
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