AMBER Archive (2004)

Subject: Re: AMBER: question about antechamber program

From: David A. Case (
Date: Fri Jul 02 2004 - 15:26:12 CDT

On Fri, Jul 02, 2004, Sivanesan Dakshanamurthy wrote:
> I was trying to siumulate protein with the cognate ligand.
> Hence, I ran the following script:
> /usr/local/fbscapp/amber8/exe/antechamber -i LIG.pdb -fi pdb -o LIG.prepin \
> -fo prepi -c bcc -nc -0 || goto error
> /usr/local/fbscapp/amber8/exe/parmchk -i LIG.prepin -f prepi -o frcmod || goto error
> /usr/local/fbscapp/amber8/exe/tleap -s -f > leap.out
> /usr/local/fbscapp/amber8/test/dacdif -t 0 LIG.prepin

This command ("dacdif") checks the differences between your result and
a "saved" result that is supposed to be the right answer. We do this for
the test suite, so that you can know whether or not your programs are giving
the answers they should be giving.

If you are running your own example, there is obviously no previously saved

> The OUTPUT Look like below:
> Total number of electrons: 208; net charge: 0
> Running: /usr/local/fbscapp/amber8/exe/divcon
> Cannot open No such file or directory

See above.

> 1. What was the problem in my input.

I don't see that there is any evidence that you had a problem.

> 2. after having the ligand parameters assigned , I
> need to add the ligand coordinates to its receptor
> file, so that complex will formed.
> At this point, how can I include the ligand parameters
> in the LEAPRC file.

You generally don't add it to the leaprc file (although you could); instead
you would issue commands like those in the "" files, such as

LIG = loadamberprep LIG.prepin
loadAmberParams frcmod

..good luck...dac

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