Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber

From: David Case <>
Date: Fri, 6 Sep 2019 12:19:47 +0000

On Thu, Sep 05, 2019, Shankha Banerjee wrote:

>But the in output PDB file, side-chain carboxylate group of ASP made a
>five-membered ring with C-terminal carbon of ASP residue when I gave
>net charge zero in Antechamber.

You always need to give the correct net charge. If gas phase
minimization gives geometries that one would not expect in solution, you
can turn off minimization, and have antechamber use the input structure
only. See Note #7 in Section 15.2 of the Amber 2019 Reference Manual.

While I gave net charge as -1 and
>multiplicity 3, the program did not run giving "fatal error".

It's always helpful to give as much of the actual error message as you
can. But antechamber charge generation is designed for closed-shell
molecules, so setting multiplicity to 3 won't do what you want.

...hope this helps...dac

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Received on Fri Sep 06 2019 - 05:30:02 PDT
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