AMBER Archive (2004)

Subject: RE: AMBER: Fe parameter

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 12 2004 - 13:19:23 CDT

Dear Hj.

> I run into a problem while I set up my simulation
> .There is a iron ion which forms several coordinate bonds
> with residues of protein.Then,where can I find the parameters
> of Fe?I have got the parameters of heme.I'm not sure whether
> that can be used on my system .

Welcome to the world of classical parameterised force fields. Your best bet
here is to look for systems that are similar to yours. If your system looks
like heme, 6 coordinate iron bound to 5 nitrogens and an oxygen then you
could try the heme iron params and see what happens. Alternatively you could
check the literature to see if anyone has published parameters for a system
with an iron atom that more closely resembles yours in terms of number of
ligands and types of ligands etc and then adapt these parameters.

> On the other hand,as the purpose of simulation is to
> optimize the structure modeled from another protein,I have
> run the simulation without iron ion while I used the
> "nmropt" to restrain the distance between the residues which
> form coordinate bonds with iron ion.Can anyone tell me
> whether it is reasonable or not?

This may be reasonable, seems like a good suggestion. I would be careful
though. Myself I would be inclined to include the iron atom but not have it
bound to anything around it. You could maybe do a resp fit of the ligands
around the iron and use those charges instead of the default charges. In
this way you can at least include the electrostatics effects of the iron
atom if not the covalent bond effects. Another option might be to guess a
few parameters, make them pretty weak and then bond the nearby ligands to
the iron instead of retraining them with nmropt. In this way you may get a
reasonable structure even if the dynamics around the iron atom are not
strictly correct.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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