Re: [AMBER] memory allocation error for *bond

From: David A Case <>
Date: Sun, 20 Jul 2014 08:05:57 -0400

On Sun, Jul 20, 2014, Vishal Nemaysh wrote:
> I am a newbie to use the AMBER 12 and after generate mol2 file i trying to
> run the command as follow:
> *antechamber -i DNA.mol2 -fi mol2 -o DNA.prepin -fo prepi*
> . I have encountered the following error massege:
> *memory allocation error for *bond*

I agree that this does not work, but it is not supposed to work, either.

1. As I said in the earlier email, try to avoid the prepi,prepc formats.
If you post a message saying why you thought you needed to to this step (i.e.
what you were trying to accomplish), someone might be able to offer better

2. antechamber is designed for *single residues*, not for entire molecules or
complexes of molecules. Unfortunately, antehcamber is among the weakest of
the AmberTools suite of programs in terms of handling bad inputs.

...good luck....dac

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Received on Sun Jul 20 2014 - 05:30:02 PDT
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