AMBER Archive (2004)

Subject: RE: AMBER: N-terminal Arg charges in ff99 not 1.00

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jun 30 2004 - 16:26:22 CDT

Dear Michael,

My terminal arginine has a charge of +2.

xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99 (AMBER8)

>check NARG
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.

What version of amber are you using? Are you certain you have loaded the
correct library files? Has somebody modified the unit in any way? If you can
let us have these details then we can try and help further.

A list of the charges on each of the atoms in the NARG residue would be
useful as well.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Michael Dolan
> Sent: 30 June 2004 14:08
> To: amber_at_scripps.edu
> Subject: AMBER: N-terminal Arg charges in ff99 not 1.00
>
> Hello Ambers,
>
> I've noticed that the total charge for a charged N-terminal
> Arginine is
> 0.9764. Can someone explain why it is not 1.00? The total
> charge of the
> Arg and it's terminal blocking group is 1.9764.
>
> Thank you,
>
> Mike
>
> --
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