AMBER Archive (2009)

Subject: Re: [AMBER] heme (united-atom)

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Nov 25 2009 - 10:39:10 CST

On Wed, Nov 25, 2009, Simon Becker wrote:
>
> I got a fivefold coordinated heme in the protein I'm investigating, and
> am subsequently using the parameter files is the /dat/contrib/heme folder:
>
> source leaprc.ff99
> loadamberparams /usr/local/amber8_64/dat/contrib/heme/frcmod.hemuni
> loadamberprep /usr/local/amber8_64/dat/contrib/heme/heme_uni.in
> prot = loadpdb "wt_ha.pdb"

First, as leap mentioned, the frcmod.hemuni file looks way out of date; I'd
recommend starting from the all-atom version.

Second, it looks(?) like the second time through you did not use loadAmberPrep
to bring in the heme*.in file.

Also, you will need to be sure that the heme atoms and residue names in
wt_ha.pdb match those in the (modified) heme_all.in file.

...good luck...dac

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