[gmx-users] molecular oxygen

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 18 18:27:27 CET 2005

On Fri, 18 Feb 2005, Cesar Lopez wrote:

>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?????????

I don't think it is there standard. It's not so hard to manually adjust 
the topology for something like this though. Check chapter 5 of the 
manual. Just add a few bonds angles and dihedrals. Problem is the force 

>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
>> Cesar
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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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