AMBER Archive (2009)

Subject: AW: [AMBER] atomtypes in gaff

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Thu Jun 25 2009 - 04:24:07 CDT

Dear Francois,
thank you very much for your fast answer.
The atomtypes should be correct.
I send you the mol2 file of the comlex from xleap.
The benzimidazole is over the N3 (nd) non physical coordinated to the zinc.
I calculate other ligands (substrate and imidazole derivative) with this
enzyme and it works.
So I think it is not a problem of zinc.
I hope, this is the file you want.
I send you also the xleap.log
Thanks!
Susanne

-----Ursprüngliche Nachricht-----
Von: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]Im
Auftrag von FyD
Gesendet: 25 June 2009 10:55
An: AMBER Mailing List
Betreff: Re: [AMBER] atomtypes in gaff

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:
http://q4md-forcefieldtools.org/Tutorial/leap.php
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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  • application/octet-stream attachment: leap.log


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