AMBER Archive (2007)

Subject: RE: AMBER: Protein containing iron.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Nov 13 2007 - 12:37:40 CST

Dear Syed,

> I am working on a protein having iron in +2 state when
> i am saving prmtop and inpcrd, it is giving the
> following error,
>
> For atom: .R<FE 591>.A<FE 1> Could not find type: FE

You are going to need to provide parameters, at the very least charge and
VDW parameters for the iron, although more likely bond, angle and dihedral
parameters as well. You should do a thorough search of the literature to see
what people have done with iron atoms in classical MD simulations of the
system you are looking at. In addition see

http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four_orig/

to get an idea of how to create your own atom types, add parameters etc.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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