AMBER Archive (2003)

Subject: Re: Re: AMBER: a problem with antechamber and leap

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 11 2003 - 19:01:39 CST

On Tue, Nov 11, 2003, Junmei Wang wrote:

> To solve this problem, you may use the following strategy:
> (1) run antechamber to get the coordinate files
> antechamber -fi pdb -fo rst -i ppi.pdb -o ppi.rst
> (2) run antechamebr to get the gaussian input file
> antechamber -i ppi.pdb -fi pdb -o ppi.gjf -fo gcrt -nc -1
> (3) run gaussian to get gaussian output file
> (4) load gaussian output file and generate an ac file
> antechamber -fi gout -fo ac -i ppi.out -fo ac -i ppi.ac -c resp (you want
> to use resp charge)
> (5) generate ppi.prepi from ppi.ac
> antechamber -fi ac -fo prepi -i ppi.ac -o ppi.prepi
> (6) prepare a new pdb file that combine atom names in ppi.ac and
> coordinates in ppi.rst
> antechamber -fi ac -fo pdb -i ppi.ac -o ppi.pdb -fa rst -a ppi.rst (for
> antechamber in amber7)
>

Junmei:

With all respect to the great work you have done, we have to find an easier
way to do this in the future :-)

I have never used the "-fa" option in antechamber, and the manual isn't
very clear (it just says "additional file", but what is it used for?). And
why is the Amber restart format chosen in steps (1) and (6) above?

Here is what I would like to see, but I don't know if it will work (yet).

(1) run antechamber to get the gaussian input file:
   antechamber -i ppi.pdb -fi pdb -o ppi.gjf -fo gcrt -nc -1

(2) run gaussian to get gaussian output file (call it ppi.out)

(3) load gaussian output file and generate a mol2 file:
    antechamber -fi gout -fo mol2 -i ppi.out -o ppi.mol2 -c resp

    [the order of the atoms in all of the above files should be the same
     as in the original pdb file]

(4) use the "loadMol2" (which is in Amber 8) to get this into LEaP.

This avoids the prep format completely, avoids reordering/renaming atoms,
and creates a mol2 format file that could be used as input to other programs
than LEaP.

What do you think?

..thanks!...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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