AMBER Archive (2009)

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

From: Simon Becker (simon.becker_at_uni-konstanz.de)
Date: Thu Nov 26 2009 - 08:34:59 CST

case schrieb:
> 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 First, as leap mentioned, the frcmod.hemuni file looks way out of date; I'd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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>
Hi all, and a happy thanksgiving.

yes I see that the frcmod and the .in files really look different, and
I'm having a hard time understanding what is what and identifying the
bits I have to change. Any pointers would be highly appreciated.

In related news: can I use leap to delete the 6th binding site of the
heme_all modell and add an additional charge? Or delete the fe's zero
order bonds? Is this even possible?

thanks
Simon 

-- 
Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647 
Universitaet Konstanz
D-78457 Konstanz 

mail: simon.becker_at_uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183

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