AMBER Archive (2008)

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

From: tinni sona (tinni.217_at_gmail.com)
Date: Wed Jul 23 2008 - 11:48:19 CDT

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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