Re: [AMBER] Prep file is empty

From: David A Case <>
Date: Wed, 29 Jan 2014 10:27:40 -0500

On Wed, Jan 29, 2014, DEBOSTUTI GHOSHDASTIDAR wrote:
> I have calculated esp charges for BF4 using gaussian G09.While converting
> the log file to the prep file using antechamber, the Fluorine atoms are not
> being recognized and NEWPDB is empty.

1. Can you give the exact command-line arguments you are using?
2. What makes you conclude that the fluorine atoms are not being recognized?

> The log file and the corresponding mol2 file are fine

If the "mol2 file is fine", can you not use that? NEWPDB is just an
intermediate file in any case. If you have the mol2 file, you should be good
to go.

I'm probably not understanding what you did, and what exactly went awry.


> Running: /usr/local/bin/amber12//bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> Running: /usr/local/bin/amber12//bin/prepgen -i ANTECHAMBER_PREP.AC -f int
> -o BF4_ani.prep -rn "MOL" -rf molecule.res

p.s. Note that antechamber doesn't know anything about boron. You'll have to
generate parameters for that on your own (or follow the instructions in
section 2.2 of tutorial A15.)

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Received on Wed Jan 29 2014 - 07:30:03 PST
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