AMBER Archive (2009)

Subject: Re: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Dec 10 2009 - 17:52:40 CST

this was a bug in the earlier version that was corrected. unclear
what effect it has- likely significant in such a small system

On 12/10/09, Dongshan Wei <dswei0523_at_gmail.com> wrote:
> Hi, All,
>
> Do you notice the difference of Amber ff03 force field between Amber8 and
> Amber10 for dipeptide ACE-ALA-NME? I found the charges of atoms from ACE and
> NME terminals are different in Amber8 ff03 and Amber10 ff03 force fields but
> the charges of atoms from ALA unit are same. The detailed charges for all
> atoms in Ala2 dipeptide are shown as follows:
>
> For Amber8 ff03 force field:
>
> %FLAG CHARGE
> %FORMAT(5E16.8)
> 2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00
> 1.08823576E+01
> -1.03484442E+01 -7.37589504E+00 5.36238555E+00 -5.05359046E-01
> 2.20129028E+00
> -4.19023611E+00 1.41091624E+00 1.41091624E+00 1.41091624E+00
> 1.03907928E+01
> -1.01157272E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00
> 1.77849648E+00
> 1.77849648E+00 1.77849648E+00
>
> For Amber10 ff03 force field:
> %FLAG CHARGE
> %FORMAT(5E16.8)
> 1.38507702E+00 -3.46702946E+00 1.38507702E+00 1.38507702E+00
> 9.33716119E+00
> -1.00253628E+01 -7.37589504E+00 5.36238555E+00 -5.05359046E-01
> 2.20129028E+00
> -4.19023611E+00 1.41091624E+00 1.41091624E+00 1.41091624E+00
> 1.03907928E+01
> -1.01157272E+01 -7.72421430E+00 5.28648968E+00 -9.89343334E-01
> 1.14235599E+00
> 1.14235599E+00 1.14235599E+00
>
> Why is the ff03 force field in Amber8 and Amber10 different? Will the
> difference of charges lead to important Ala2 conformation difference?
>
> Thanks!
>
> Dongshan
>
> -----------------------------------------------------------------------------------
> Dr. Dongshan Wei
> Department of Chemistry
> Boston University
> Boston, MA, 02215
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80           Phone: (631) 632-1336   Fax: 632-1555
Stony Brook University           E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
===================================================================

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