[gmx-users] Metalloprotein simulation

[David van der Spoel]

On Thu, 2003-03-27 at 10:48, Ranjit Sudhakar Ranbhor wrote:
> Hi,
> 
> Have anybody used Gromacs for metalloprotein simulation (other than Zn)? I
> am trying to do MD for nonheme iron (FE2+) protein. But when I looked into
> ffgmxnb.itp, there are no (ie assigned zero) C6 and C12 parameters defined
> for FE (although FE is present in ffgmx.atp). Is there any particular
> reason why C6 and C12 parameters for FE are 0 in ffgmxnb.itp? Also if I
> have to get these parameters for FE, how should I proceed for the same?
> 
This is difficult. You can probably estimate something based on other
parameters (for other ions), but it will also depend on the ligands, the
oxidation state of the Iron and so on...

If you manage to find sigma and epsilon that maintain the right ligation
bonds and angles you are in good shape, but you will have to do some
testing...

Start out with e.g. Zn parameters and then modify sigma and epsilon
(C6/C12) until your iron center is stable in say, a 100 ps simulation...
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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