AMBER Archive (2004)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 01 2004 - 14:17:02 CDT

Dear Mike,

With FF94 I still get a charge of +2.000000 for NARG:

Amber8:
xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff94

Welcome to LEaP!
Sourcing: /usr/local/amber8/dat/leap/cmd/leaprc.ff94
Log file: ./leap.log
Loading parameters: /usr/local/amber8/dat/leap/parm/parm94.dat
Loading library: /usr/local/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber8/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber8/dat/leap/lib/solvents.lib
> check NARG
Checking 'NARG'....
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
Checking parameters for unit 'NARG'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
>

What version of amber are you using? How are you checking the charge? What
library files are you loading? - Are you certain your amber installation has
not been modified?

All the best
Ross

/\
\/
|\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: 01 July 2004 12:01
> To: amber_at_scripps.edu
> Subject: Re: AMBER: N-terminal Arg charges in ff99 not 1.00
>
> Sorry, I made a mistake. I meant to say that the total charge for a
> charged N-terminal Arg is 1.9764 in ff94. It is 2.00 in ff99. Why is
> there a difference? Is this just a result of rounding or has
> the charge
> been corrected in ff99? I am looking at Arg in all_aminont94.in.
>
> Thank you,
>
> Mike
>
>
> Guanglei Cui wrote:
> >
> > What version of amber are you using? For amber8, "charge
> NARG" gives me
> > 2.00 ...
> >
> > Guanglei
> >
> > Michael Dolan wrote:
> >
> > > 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
> > >
> >
> --------------------------------------------------------------
> ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu