AMBER Archive (2007)

Subject: AMBER: Running Gaussian to get .out files

From: Steve Spronk (spronk_at_umich.edu)
Date: Fri Aug 24 2007 - 09:08:13 CDT

Hi Lili,

 

Yes, the input does matter very much. From your original post I assumed
that you had already performed step 2 of the procedure, in which you convert
your mol2 files to Gaussian input files. Gaussian has a very specific input
format and won't run if you don't supply the correct format.

 

As for the output file, it doesn't matter what the file extension is, but
the format will conform to the standard Gaussian output file format. This
is the file that you should use as the input to the espgen command in step
4.

 

Steve

 

  _____

From: Lili Peng [mailto:lilipeng_at_gmail.com]
Sent: Thursday, August 23, 2007 3:44 PM
To: spronk_at_umich.edu
Subject: Re: AMBER: Running Gaussian to get .out files

 

Hi Steve,

Thanks for your response. Just to emphasize, does it matter what format my
input file is in (.mol2 or .ac)? Also, my output file is in .out format?
Case in point:

$ g03 <glu3.mol2> glu3.out &

Thanks for your help again,
Lili

On 8/23/07, Steve Spronk <spronk_at_umich.edu> wrote:

Hi Lili,

 

Gaussian can be run like this:

 

$ g03 < inputfile > outputfile &

 

Also, you could consider obtaining resp charges using the program RED. I
have had a lot of success with it. It automates the execution of Gaussian
and the program resp, and you don't have to deal with any of the file
conversions yourself.

 

Steve

 

  _____

From: owner-amber_at_scripps.edu [mailto: <mailto:owner-amber_at_scripps.edu>
owner-amber_at_scripps.edu] On Behalf Of Lili Peng
Sent: Wednesday, August 22, 2007 4:27 PM
To: amber_at_scripps.edu
Subject: AMBER: Running Gaussian to get .out files

 

Hi,

I am trying to do the Antechamber tutorial on non-standard amino acid
residues (http://amber.scripps.edu/antechamber/pro4.html), and I am stuck on
Step 3: Run gaussian to get two output files. Does anyone know how I go
about getting .out files from my .gau files?

Thanks in advance,
Lili

 

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