AMBER Archive (2008)

Subject: Re: AMBER: 3fe-4s cluster parameter file generation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Sep 15 2008 - 13:51:29 CDT

> 1 DUMM DU M 999.000 999.0 -999.0 .00000
> 2 DUMM DU M 999.000 -999.0 999.0 .00000
> 3 DUMM DU M -999.000 999.0 999.0 .00000
> 4 S1 S S 0.402592 -1.514288 -1.117435 -0.15436
> 5 S2 S S -1.882611 0.670231 -0.727350 -0.17413
> 6 S3 S B 0.078709 -0.205500 1.731896 -0.31438
> 7 S4 S S 1.046182 1.057400 -1.309825 -0.13664
> 8 FE1 FE B -1.129336 -1.094156 0.156620 0.63632
> 9 FE2 FE B 1.553155 -0.302094 0.294594 0.59276
> 10 FE3 FE B -0.205279 1.391423 0.424303 0.55042

Looking at the doc of the prep format:

  http://amber.scripps.edu/doc/prep.html

I think you have something like

S-S-S-S-Fe
      |
      Fe-Fe

What bonds are you trying to create? Maybe something like this:

S-S-S-S-Fe
  | |
 Fe Fe

In which case the topological types might be:

M-M-M-M-E
  | |
  E E

And the order of atoms:

1-2-4-6-7
  | |
  3 5

This may help you think out your structure in any case.

Bill
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu