AMBER Archive (2008)

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

From: moitrayee_at_mbu.iisc.ernet.in
Date: Mon Sep 15 2008 - 06:46:56 CDT

I did not use antechamber but manually did it using the co-ordinate and charge
information from the Gaussian single point calculation. The prepc file is given
below:

    0 0 2

This is a remark line
molecule.res
F3S XYZ 0
CHANGE OMIT DU BEG
  0.0000
   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 M 0.402592 -1.514288 -1.117435 -0.15436
   5 S2 S M -1.882611 0.670231 -0.727350 -0.17413
   6 S3 S M 0.078709 -0.205500 1.731896 -0.31438
   7 S4 S M 1.046182 1.057400 -1.309825 -0.13664
   8 FE1 FE M -1.129336 -1.094156 0.156620 0.63632
   9 FE2 FE M 1.553155 -0.302094 0.294594 0.59276
  10 FE3 FE M -0.205279 1.391423 0.424303 0.55042

LOOP

IMPROPER

DONE
STOP
And the frcmod file is as follows:

remark goes here
MASS
S 32.060 same as ss
FE 55.000 ATTN, need revision

BOND

ANGLE

DIHE

IMPROPER

NONBON
  S 2.0000 0.2500 same as ss
  FE 1.2000 0.0500 ATTN, need revision
This are the files that i use. Please let me know what i can do ?

Sincere Regards,
Moitrayee

> On Mon, Sep 15, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:
>
>> I prepared the .prepc file for the cluster...
>
> You don't say how you got the prepc file. If you used antechamber, I
> will just repeat what was said earlier: antechamber won't work for
> transition metals. You will have to prepare the unit by hand.
>
> ...dac
>
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