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

From: Pengfei Li <ambermailpengfei.gmail.com>
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:
http://www.pharmacy.manchester.ac.uk/bryce/amber/

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.
http://onlinelibrary.wiley.com/doi/10.1002/jcc.20079/full
http://onlinelibrary.wiley.com/doi/10.1002/jcc.20221/full
http://onlinelibrary.wiley.com/doi/10.1002/jcc.21922/full

HTH,
Pengfei

On Oct 29, 2014, at 12:31 AM, Saeed Nasiri <s.t.nasiri.gmail.com> 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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> AMBER.ambermd.org
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Received on Wed Oct 29 2014 - 13:00:04 PDT