Re: [AMBER] antechamber

From: Mark Williamson <>
Date: Wed, 20 Aug 2014 13:04:48 +0100

On 20/08/14 12:41, Jason Swails wrote:
> On Wed, 2014-08-20 at 10:31 +0800, 闫玉娜 wrote:
>> Hi all,
>> I have a small molecule named 'HEM'. I want to use antechamber to build its
>> parameters. I use the command 'antechamber -i HEM_ideal.pdb -fi pdb -o
> Alternatives are: look to see if your Heme complex has already been

Re AMBER heme parameters; this paper might a good starting point;
especially the rich supporting material:

"Quantum mechanically derived AMBER-compatible heme parameters for
various states of the cytochrome P450 catalytic cycle."
Kiumars Shahrokh, Anita Orendt, Garold S. Yost and Thomas E. Cheatham III



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Received on Wed Aug 20 2014 - 05:30:02 PDT
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