AMBER Archive (2003)

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

From: Junmei Wang (JWang_at_encysive.com)
Date: Wed Nov 12 2003 - 14:46:02 CST

Hi, Dave,

If the mol2 format works well in leap, we may forget prep input file. With
mol2 file, one doesn't need to worry about the atom sequence/atom names
issue.
By the way, I introduced " -a " in antechamber when I were working on force
field development: with this feature, I can easily get the minimized
structure (in pdb) without using carnal.

Best regards

Junmei

===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             "David A. Case"
             <case_at_scripps.edu
> To
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             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       Re: Re: AMBER: a problem with
             11/11/2003 07:01 antechamber and leap
             PM
                                                                           
                                                                           
             Please respond to
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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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