AMBER Archive (2008)

Subject: Re: AMBER: Query about the charge of atoms in the parmtop file

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jul 23 2008 - 12:16:09 CDT

you should probably check the papers on the charge derivation for the
force field that you used (you don't say which).
terminal residues often have a formal charge, which affects the atom charges.

On Wed, Jul 23, 2008 at 12:48 PM, tinni sona <tinni.217_at_gmail.com> wrote:
> Hi All,
>
> I want to perform a MD simulation of protein-carbohydrate complex. I
> used Leap to generate the prmtop and inpcrd files. It is given in
> http://amber.scripps.edu/formats.html#topo.cntrl that in parmtop file
>
> FORMAT(5E16.8) (CHRG(i), i=1,NATOM)
> CHRG : the atom charges. (Divide by 18.2223 to convert to charge
> in units of the electron charge)
>
> To match the description I was taking a look on the charges of
> individual atoms in the parmtop file for my system. I noticed that
> except the atoms of terminal residues of the protein (N ter and C-ter
> residues) all the atoms in the other residues following the same and
> giving the exact value of charge.
> Now my question is for the atoms of terminal residues of protein why
> the charge values are differing ?
>
> I also have a look on the " amber9/benchmarks/gb_alp" in AMBER9 and
> here in parmtop file also I noticed the same as I obtain for my
> system.
>
> I simply can't understand why it is happening so.
>
> I will be highly obliged if you could respond.
>
> Thanks and regards,
> Madhurima
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-- 
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