AMBER Archive (2009)

Subject: [AMBER] iron in prepi file generation for heme

From: Donald Keidel (dkeidel_at_scripps.edu)
Date: Wed Dec 23 2009 - 16:27:10 CST

Hello,

I have generated resp charges using gaussian and antechamber. I am trying to generate a prepi file that will include the Fe atom information for heme.

I am getting the following error message when I execute the following command:

command I execute: antechamber -fi mol2 -fo mol2 -i
HEM_edited_H_pmv_marvin_babel.mol2 -o
HEM_edited_H_pmv_marvin_babel_resp.mol2 -c rc -cf input.crg -j 4 -at amber

error: For atom[1]:Fe, the best APS is not zero, bonds involved by this
atom are frozen

I then look at a prepi file I create from this output and see the following line:

   78 X 1 0 1 3.450 nan 0.000 0.000000

I have omitted many lines for the sake of the email length.

I think I can maybe add Fe to the APS.dat file (I have done this with Se atom before) but I do not know what to
add for all the columns. I have tried looking for this information in the archives and google with no luck. Can you let me know exactly what to add to the
APS.data file if this is the correct way to proceed? Otherwise, what are my other options.

Thank you very much.

Don

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