Re: AMBER: modifications to force field for Fe4S4 cubane

From: David A. Case <>
Date: Tue, 27 Nov 2007 13:10:40 -0800

On Tue, Nov 27, 2007, Ilyas Yildirim wrote:

> I do not think that you can have 1 FES and 4 CYS residues where CYS residues
> are connected to 4 different atoms of FES residue.

Of course you can do this.

Here is a file we use for iron-sulfur clusters:

source leaprc.ff99SB
addAtomTypes {
  {"FS" "Fe" "sp3"}
  {"SM" "S" "sp3"}
  {"SB" "S" "sp3"}
loadamberparams frcmod.fe4s4
1IUA = loadPdb 1IUA.mN.pdb
bond 1IUA.84.FE1 1IUA.43.SG
bond 1IUA.84.FE2 1IUA.46.SG
bond 1IUA.84.FE3 1IUA.61.SG
bond 1IUA.84.FE4 1IUA.75.SG
solvateOct 1IUA TIP3PBOX 12.0 0.75
saveamberparm 1IUA prmtop prmcrd


"CYF" is a modified cysteine (with no HG atom); "FS4" is the iron sulfur
cluster. The "bond" commands connect the cysteine residues to the cluster.

It's hard to help the original poster, since the emails are very confusing.
It's never clear *exactly* what was done, and what the error message was.


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Received on Wed Nov 28 2007 - 06:07:40 PST
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