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
suggestions.
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
