[AMBER] Zinc Paramitarization

From: Patrick Appiah-Kubi <appiahpat.gmail.com>
Date: Thu, 9 Oct 2014 10:02:28 +0200

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 1AMP_OH_sidechain_opt_md.com -l 1AMP_OH_sidechain_opt_md.com.log

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. (214584533.stu.ukzn.ac.za)

Kind regards
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Received on Thu Oct 09 2014 - 01:30:02 PDT
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