AMBER Archive (2002)

Subject: Re: esp.sh problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 27 2002 - 13:12:54 CST

On Wed, Nov 27, 2002, FyD wrote:
>
> I am trying to use "esp.sh" from
> http://www.amber.ucsf.edu/amber/Questions/resp.txt...

>
> tot 1% esp.sh test.out
> enter natom,nesp: startio: error in format
> apparent state: unit 5 (unnamed)
> last format: (2i)

The problem is that "(2i)" is not a legal format for many fortrans. Go into
readit.f, and change the line:

      read (5,'(2i)') i,j
to
      read (5,*)i,j

and recompile.

This problem has been fixed in amber7/src/resp/readit.f. As is not
uncommon, keeping the web page up to date has slipped between the cracks...

Also, it's worth noting that the recommended way to do resp now (at least
if you don't need multiple conformer fitting) is to use antechamber. This
provides a very easy way to generate the input needed for Gaussian, and parses
the Gaussian output and runs it through resp, putting the charges into the
right place at the end. (It is essentially doing internally the same work
as esp.sh.)

Generally, what you need to do is the following:

   antechamber -i {name}.pdb -fi pdb -o {name}.in -fo gcrt
   g98 < {name}.in > {name}.log
   antechamber -i {name}.log -fi gout -o {name}.prepi -fo prepi -c resp

This will give you a prep input file with the resp charges included. Options
are available in antechamber for using other sources of input (besides pdb)
and other formats of output (besides prepi).

We do have a project ongoing to massively update the FAQ's, and will get this
fixed up as well.

..hope this helps....dac 

-- 

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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:                   
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