AMBER Archive (2009)

Subject: [AMBER] atomtypes in gaff

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Thu Jun 25 2009 - 01:49:48 CDT

Hello amber users,
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

 <<bzim_correct.mol2>> <<bzim_correct.prepin>> <<bzim_wrong.mol2>>
<<bzim_wrong.prepin>> <<c2k_bzim_correct.pdb>> <<c2k_bzim_wrong.pdb>>








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