On Fri, Nov 20, 2015, Ayesha Kanwal wrote:
>
> i am using antechamber and creating parameter and coordinate files for 1IMX
> for creating mol2 file i give the following command i rename my insulin
> protein 1IMX with sustiva after that when i run this command it generate
> an error
> /Desktop/Softwares/amber14/bin/1mx$ antechamber -i sustiva_new.pdb -fi
> pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
Antechamber is intended to help with getting parameters for *small organic
molecules*, not for proteins.
Please follow the tutorials (e.g. tutorial B0) for information about how to
set up proteins in Amber. Be sure to use pdb4amber on the input file, to
remove non-protein components (which in this case you probably don't want).
...good luck....dac
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Received on Fri Nov 20 2015 - 05:00:03 PST
