[gmx-users] molecular oxygen

[David van der Spoel]

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 
constants.


 > 
>Thank for your time
>Cesar
>
>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
>> 
>> __________________________________________________
>> Do You Yahoo!?
>> Tired of spam? Yahoo! Mail has the best spam protection around 
>> http://mail.yahoo.com 
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>

-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++