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First, as leap mentioned, the frcmod.hemuni file looks way out of date; I'd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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Received on Wed Nov 25 2009 - 09:00:02 PST
