[AMBER] Parametrization of Small Molecules

From: Johannes Loeffler <johannes.r.loeffler.gmail.com>
Date: Fri, 18 May 2018 11:44:56 +0200

Dear All,

I am trying to parametrize small molecules for free energy calculations.
However, in the antechamber step the atoms in the resulting mol2 file
are renamed and reordered. The command I used:

antechamber -i 13a.log -fi gout -o 13_test.mol2 -fo mol2 -c resp -a
13a.pdb -ao pdb -at gaff -nc 1 -rn 13a

Is there a reason why antechamber does not take the names from the
specified pdb file, or is there something wrong with my command?

Thank you in advance,

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Received on Fri May 18 2018 - 03:00:02 PDT
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