AMBER Archive (2009)

Subject: [AMBER] Re: bug in antechamber

From: David Mobley (dlmobley_at_uno.edu)
Date: Mon Jul 13 2009 - 12:41:01 CDT

Junmei and all,

I just wanted to check in on this -- did you receive it? I didn't
receive any response.

Thanks.

On Jul 8, 2009, at 11:19 AM, David Mobley wrote:

> Dear Junmei and all,
>
> I believe I have found a bug in Antechamber/AmberTools (i.e. v. 1.27
> of Antechamber, and also the more recent AmberTools release).
>
> In particular, see the attached three mol2 files and try the
> following sequence of commands:
>
> antechamber -i 4-vinylpyridine_am1bcc_sybyl.mol2 -o out_sybyl.mol2 -
> fi mol2 -fo mol2 -c bcc -at sybyl
> antechamber -i 4-vinylpyridine_am1bcc_sybyl.mol2 -o out_sybyl_1.mol2
> -fi mol2 -fo mol2 -c bcc -at sybyl -j 1
>
> (These two output files are attached, as is the input file).
>
> In this case, the -j 1 option actually has no effect on atom/bond
> typing as far as I can tell, as the output atom/bond types are the
> same regardless of whether the j option is used.
>
> HOWEVER (and here is the problem!) the -j 1 option has a huge effect
> on the partial charge on the nitrogen atom.
>
> Please advise.
>
> Thanks,
> David
>
>
> <out_sybyl.mol2><out_sybyl_1.mol2>
>
>
> <4-vinylpyridine_am1bcc_sybyl.mol2>
>
>
> David Mobley, Ph.D.
> Assistant Professor of Chemistry
> University of New Orleans
> New Orleans, LA 70148
> dlmobley_at_uno.edu
> Office 504-280-6445
> Fax 504-280-6860

David Mobley, Ph.D.
Assistant Professor of Chemistry
University of New Orleans
New Orleans, LA 70148
dlmobley_at_uno.edu
Office 504-280-6445
Fax 504-280-6860

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