Re: [AMBER] problem with antechamber in ambertools 13

From: David A Case <>
Date: Wed, 4 Sep 2013 08:41:51 -0400

On Tue, Sep 03, 2013, Rodrigo Salazar wrote:
> I am trying to run antechamber using ambertools 13 for this molecule:
> antechaber -i b.pdb -fi pdb -o b.mol2 -fo mol2 -c bcc -at amber -nc -1
> and I get the following error:
> Error: cannot run "/home/rodrigo/amber12/bin/sqm -O -i -o sqm.out"
> of bcc() in charge.c properly, exit

Works for me: what version of AmberTools do you have?

In any event, you should look at the sqm.out file to see what the error is.
Also, are you sure you want amber atom types?

[Scott: can you add a instruction to "look at the sqm.out file for more
information" (or similar wording) to the error message above?]

[Junmei: the notion of "Amber atom types" no longer has its old meaning, back
when the Cornell libraries were about the only ones we had. Now the number
and description of Amber atom types depends a lot of which Amber force field
one is using. Should we consider removing this option? Or can it be updated
to refer to a specific Amber force field?]


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Received on Wed Sep 04 2013 - 06:00:06 PDT
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