AMBER Archive (2009)

Subject: Re: [AMBER] total charge for NPRO in ff03ua

From: Edyta Malolepsza (em427_at_cam.ac.uk)
Date: Tue Jun 16 2009 - 04:42:55 CDT

Dear Jun,

Thank you for sending the correct atomic charges. It may be good to
correct the file uni_aminont03.lib in next release of AMBERTools.

Best wishes,

Edyta Malolepsza

On Tue, Jun 16, 2009 at 12:35 AM, Jun Wang<jwang20_at_uci.edu> wrote:
> Dear Edyta,
>
> The total charge of PRO should be an integer. The correct charges of H2 and
> H3 are both 0.471856.
>
> Best,
> Jun Wang
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
> Of Edyta Malolepsza
> Sent: Monday, June 15, 2009 3:10 AM
> To: AMBER Mailing List
> Subject: [AMBER] total charge for NPRO in ff03ua
>
> Dear Amber users,
>
> I am using the united atom force field ff03ua and have come across a
> problem with N-terminal proline, where total charge for the whole
> residue is not integer. Here is an entry from uni_aminont03.lib. This
> entry is the same both for amber9 and amber10 taken from latest
> version of AMBERTools1.2 from AMBER10.
>
> !entry.NPRO.unit.atoms table str name str type int typex int resx
> int flags int seq int elmnt dbl chg
> "N" "N" 0 1 131072 1 7 -0.415266
> "H2" "H" 0 1 131072 2 1 0.418633
> "H3" "H" 0 1 131072 3 1 0.418633
> "CD" "C2" 0 1 131072 4 6 0.179220
> "CG" "C2" 0 1 131072 5 6 0.048036
> "CB" "C2" 0 1 131072 6 6 0.002419
> "CA" "CT" 0 1 131072 7 6 0.157515
> "HA" "H1" 0 1 131072 8 1 0.003120
> "C" "C" 0 1 131072 9 6 0.680470
> "O" "O" 0 1 131072 10 8 -0.599226
>
> The total charge is 0.893554.
>
> Can anybody help to explain this? All other residues have integer total
> charges.
>
> Best regards,
>
> Edyta Malolepsza

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