AMBER Archive (2007)Subject: Re: AMBER: modifications to force field for Fe4S4 cubane
From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 27 2007 - 15:10:40 CST
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 leap.in file we use for iron-sulfur clusters:
source leaprc.ff99SB
addAtomTypes {
{"FS" "Fe" "sp3"}
{"SM" "S" "sp3"}
{"SB" "S" "sp3"}
}
loadoff CYF.off
loadoff FS4.off
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
quit
"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.
....dac
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