AMBER Archive (2009)

Subject: Re: [AMBER] atomtypes in gaff

From: FyD (
Date: Thu Jun 25 2009 - 03:55:03 CDT

Dear Susanne,

In the GAFF paper, it is said:
na SP2 nitrogen with 3 substituants
nc(nd) inner SP2 nitrogen in conjugated ring sytem, 2 substituants

My feeling is that if you could provide only mol2 files with GAFF
force field atom types instead of mol2 files without GAFF force field
atom types + prepin with GAFF force field atom types, this would help
to more efficiently look at your problem. To generate a mol2 file with
FF atom types, please, see:
In short: savemol2 unit mol2filename 1

Could you describe the type of connection you wish to establish
between your organic molecule & this Zinc atom (physical connection or
no physical connection, which atom(s) in the organic structure is
involved, etc...)

regards, Francois

> At this time I coludn't solve the problem with benzimidazole coordination on
> zinc. (first query: zinc coordination of benzimidaole).
> I think the problem is in the gaff force field. Do you know what is the
> different between "na" = "N" "sp2" and "nd" = "N" "sp2" ?
> When I claculate the complex with a wrong benzimidazole structure, then the
> ligand is coordinated after minimization, when the benzimidazole is chemical
> correct built, the ligand isn't coordinated after minimization (I work with
> Amber10) Is this a problem of cheges or atomtypes? The bcc charges look
> normal.
> I couldn't send all files (this is too much) At first the antechamber files
> and the complex.pdb.
> Thanks a lot for your help!
> Susanne

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