[gmx-users] molecular oxygen
inmuno_cl at yahoo.com
Fri Feb 18 17:56:03 CET 2005
Ok, Thank you for the advice, but does gromacs support the Hem join with oxygen?????? or it is necessary to built an independent .itp file??????? How can I do that?????????
Thank for your time
David van der Spoel <spoel at xray.bmc.uu.se> wrote:
On Thu, 2005-02-17 at 10:07 -0800, Cesar Lopez wrote:
> Dear Gromacs users:
> I am working with de haemoglobin in the R and T
> states, mi question is about the molecular oxigen when
> the haemoglobin is oxygenize, Is the topology of that
> molecule in the forcefield gromos 96? Has Anybody
> worked with this molecule before?.
Not worked, but it is tricky. Since the Iron polarizes the oxygen, your
best bet may be to model the molecule as being covalently bound to the
iron, rather than an independent non-polar molecule.
> Thank you in advance
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David van der Spoel, PhD, Assoc. 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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