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.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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jul 27 2008 - 06:07:15 PDT
