AMBER Archive (2008)

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

From: moitrayee_at_mbu.iisc.ernet.in
Date: Mon Sep 15 2008 - 10:36:31 CDT

I have modified the prepc file as :-

   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 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

LOOP

IMPROPER

DONE
STOP
The pdb of the ligand is as follows:

ATOM 22415 FE1 F3S 2476 22.031 131.687 125.051 1.00 3.44 FE
ATOM 22416 FE3 F3S 2476 19.837 133.121 124.065 1.00 8.66 FE
ATOM 22417 FE4 F3S 2476 22.106 132.579 122.776 1.00 2.99 FE
ATOM 22418 S1 F3S 2476 19.888 131.269 124.910 1.00 16.32 S
ATOM 22419 S2 F3S 2476 21.822 130.489 123.262 1.00 18.57 S
ATOM 22420 S3 F3S 2476 21.887 133.677 124.533 1.00 26.75 S
ATOM 22421 S4 F3S 2476 20.081 132.614 122.029 1.00 28.82 S
But even then i am getting the same error asking for an fe-fe bond length
parameter,etc while trying to create the topology files using Leap. Please
suggest me what should i do ?

Sincere Regards,
Moitrayee

> On Mon, Sep 15, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:
>
>> 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
>
> The above is wrong: you have every atom as a "mainchain" atom, so the
> covalent structure implied above is S1-S2-S3-S4-Fe1-Fe2-Fe3, which is,
> of course, not what you want.
>
> ...dac
>
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