Re: [AMBER] Zinc Paramitarization

From: Pengfei Li <>
Date: Thu, 9 Oct 2014 11:25:50 -0400

Hi Patrick,

On Oct 9, 2014, at 4:02 AM, Patrick Appiah-Kubi <> wrote:

> Dear all,
> I am new on Amber and working on the enzyme LTA4H, which has a catalytic Zn
> metal and a Catalytic water. The Zinc is coordinated with His 295, His 299
> and a Glu138. I to paramaterize for the metal before minimization.
> I am doing the amber MCPB tutorial found at Amber tutorial, before i try
> with my enzyme. I am stuck at the step 6.
> I need to generate these files: 1AMP_OH_sidechain_opt_md.chk and
> 1AMP_OH_sidechain_opt_md.log files. I run the command below and the above
> files were not generated.
> MCPB -i -l

For this step, you should use Gaussian but not MCPB to run the calculation of file.
Afterwards you can get the 1AMP_OH_sidechain_opt_md.chk and 1AMP_OH_sidechain_opt_md.log files.

> I will also appreciate help from colleagues who have work on such Zn
> coordinated enzymes.
> I need help with scripts and commands. if anyone can also send me MCPB
> manual i will appreciate it much. (

There is no specific manual for MCPB. There is one for MTK++ (named MTKpp.pdf), which is under $AMBERHOME/AmberTools/src/mtkpp/doc/ directory.

You can check it there.

> Kind regards
> Patrick

Hope it helps,

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Received on Thu Oct 09 2014 - 08:30:05 PDT
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