[gmx-users] compound-I/II topology, i.e. porphyrin(Fe=O)
David van der Spoel
spoel at xray.bmc.uu.se
Fri Apr 9 12:00:01 CEST 2004
On Fri, 2004-04-09 at 10:35, Arturas wrote:
> I want to make a topology file for heme with oxygen atom bound to Fe,
> i.e. compound-I/II model of oxireductases. PRODRG server supports N,
> C, O, S, P, Cl, I, Br, F atoms only. So PROFRG can not help me. How to
> solve that problem.
> Should it be done by hand modifying standart heme tolopogy ? What are
> parameteres for >Fe=O fragment ?
Yes, you can do it in the rtp file. Parameters are the problem, although
there must be some quantum calculations done on similar systems, from
which you should be able to deduce charges.
> Any tricks and advises.
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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