AMBER Archive (2008)

Subject: Re: AMBER: question about antechamber

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Jan 03 2008 - 09:18:34 CST

You didn't add hydrogen atoms. To make antechamber perform soundly, please
make sure no open valence in the input molecules.

Best

Junmei

On Jan 3, 2008 8:32 AM, Lynn <lynn.non_at_gmail.com> wrote:

> dear all:
> I am doing the job about the interaction of dioxin and protein. but when i
> use antechamber to deal with 2,3,7,8-tcdd, the input format is pdb, and the
> output format is prepi, it cause problem. I read the output file, it defined
> carbon on the benzene ring as "ce" or "cc", not "ca"(as described in
> $AMBERHOME/dat/antechamber/ATOMTYPE_GFF.DEF). And such condition caused
> problem when i load frcmod file to leap, and coming-up procedure with
> protein-tcdd complex. Then i use saved prmtop and inpcrd file to run
> minimise and equilibrate, I found that the tcdd in complex would distort and
> it cannot keep as a planar construction.
>
> can any one help me?
> Or, is there any anther way to treat protein-ligand 's pdb file , make
> it analyzed correctly by leap, and do following MD simulation?
>
> thanks.
>
> Both tcdd.pdb and tcdd.prepin are attached.
>

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