AMBER Archive (2009)

Subject: Re: [AMBER] Regd: parameter Fe4S4

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Jun 29 2009 - 14:03:22 CDT

Kirtana,

I quickly looked at your d.off library.

- you have many problems of charge equivalencing:
For instance the position ortho & ortho' of your pseudo
thio-aromatic-derivative should be equivalenced. I do not understand
how you can have a charge value of -.42 & +.03 for these positions
ortho & ortho'
- same remark for many positions meta.

- you have many carbons with the c3 atom type without hydrogen.

- your FF library looks quite distorded. In principle this is not a
problem if the Cartesian coordinates of your MD initial structure are
corrected. However, this might reveal deep problems in your force
field library building.

regards, Francois

> My structure consists of a core Fe-S cluster with fe linked to dendrimer
> arms ( benzene rings with ether linkages and terminated with carboxyl
> group).
>
> I tried to generate the frcmod file using antechamber using parmchk :
> parmchk -i file.mol2 -f mol2 -o frcmod
>
> it gives me error as ATTN NEEDS REVISION.
>
> I would like to have your suggestion regarding how should I generate the
> frcmod file if I have my model in place of cysteine linkages with the
> ferrous sulphide cluster .
> In my model the sulphur in C-S-Fe link. My Carbon is a part of the benzene
> ring. Can anybody suggest what modifications I should go for in my .frcmod
> file or how should I generate my parameter file since antechamber does not
> like it .
> Below I have text of my leap log file and I have attached the library file
> of my model.(I have used the frcmod.fe4s4 file from Dr. David Case group
> where the sulphur was linked to CYS )
>
>> gaff = loadamberparams gaff.dat
> Loading parameters: /usr/local/apps/amber9/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic mol., add. info. at the end (June,
> 2003)
>
>> loadoff d.off
> Loading library: ./d.off
> Loading: d
>> edit d
>> loadamberparams frcmod1
> Loading parameters: ./frcmod1
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
>
>> loadamberparams frcmod2
> Loading parameters: ./frcmod2
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
>> loadamberparams frcmod4
> Loading parameters: ./frcmod4
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> (UNKNOWN ATOM TYPE: Fe)
>> loadamberparams frcmod.fe4s4
> Loading parameters: ./frcmod.fe4s4
> Reading force field modification type file (frcmod)
> Reading title:
> parameters for Fe4S4S(CH3)4 2-
> (UNKNOWN ATOM TYPE: SB)
> (UNKNOWN ATOM TYPE: SM)
> (UNKNOWN ATOM TYPE: FS)
>> check d
> Checking 'd'....
> WARNING: There is a bond of 20.058054 angstroms between:
> ------- .R<T111 1>.A<S1 11> and .R<FS4 12>.A<FE1 1>
> WARNING: There is a bond of 77.848345 angstroms between:
> ------- .R<FS4 12>.A<FE4 4> and .R<T111 35>.A<S1 11>
> WARNING: There is a bond of 35.327556 angstroms between:
> ------- .R<FS4 12>.A<FE3 3> and .R<T111 24>.A<S1 11>
> WARNING: There is a bond of 4.524847 angstroms between:
> ------- .R<T111 13>.A<C2 3> and .R<T111 13>.A<S1 11>
> ERROR: The unperturbed charge of the unit: 0.250400 is not integral.
> WARNING: The unperturbed charge of the unit: 0.250400 is not zero.
> Checking parameters for unit 'd'.
> Checking for bond parameters.
> Could not find bond parameter for: sh - FS
> Could not find bond parameter for: FS - sh
> Could not find bond parameter for: FS - sh
> Could not find bond parameter for: FS - sh
> Checking for angle parameters.
> Could not find angle parameter: sh - FS - SB
> Could not find angle parameter: sh - FS - SB
> Could not find angle parameter: sh - FS - SB
> Could not find angle parameter: c - sh - FS
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: SB - FS - sh
> Could not find angle parameter: FS - sh - c
> Could not find angle parameter: FS - sh - c
> Could not find angle parameter: FS - sh - c
> There are missing parameters.
> check: Errors: 1 Warnings: 5
>
>
> Thanks and Regards
> Kirtana
>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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