AMBER Archive (2008)

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

From: moitrayee_at_mbu.iisc.ernet.in
Date: Wed Sep 17 2008 - 01:43:49 CDT

I have manually prepared the prepc file from my gaussian single point energy
calculation. I have taken the standard orientation of the gout file and the ESP
charges and prepared the prepc file. I really dont know how to manage this thing
and i am getting unwanted bonds in my ligand.

Please Help with a suggestion.
Sincere Regards
Moitrayee

>> > WARNING: There is a bond of 3.265214 angstroms between:
>> > ------- .R<F3S 1453>.A<S3 3> and .R<F3S 1453>.A<S4 4>
>> > WARNING: There is a bond of 3.432639 angstroms between:
>> > ------- .R<F3S 1453>.A<S2 2> and .R<F3S 1453>.A<S3 3>
>>
>> Looks like you have some long bonds in your prep file - do these agree
>> with experiment?
>
> Note that you have S2-S3 and S3-S4 bonds. That doesn't match the
> topology picture you sent, which has alternating S/Fe in a ring.
>
> Bill
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