Re: [AMBER] How do MCPB make sidechain.bcl?

From: Pengfei Li <>
Date: Wed, 29 Oct 2014 15:50:22 -0400

Hi Alavi,

There is available parameters online and it may take a lot of time to parameterize the heme and surrounding residues
again to use MCPB. Heme group is not a standard residue and it may need more skills to parameterize it using MCPB.

You can check the force field on the website:

Please check the emails I just replied to Kevin Murphy.
There are some tips about using the parameters.

You can also check the parameters in these papers, which may be helpful.


On Oct 29, 2014, at 12:31 AM, Saeed Nasiri <> wrote:

> Hi .all
> I have some difficulties in MCPB. I can't make NAME_sidechain.bcl for my
> system. the system is Heme group and other resiude connect with it.
> I don't know I separated heme structure or not!
> can anybody help me to handle it ?
> Is there any manual for making structure file bcl?
> Best regard
> F. Alavi
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Received on Wed Oct 29 2014 - 13:00:04 PDT
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