AMBER Archive (2008)

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

From: tinni sona (tinni.217_at_gmail.com)
Date: Thu Jul 24 2008 - 02:19:26 CDT

Hi,

I'm using leaprc.ff03 for protein and leaprc.GLYCAM_06 for the
carbohydrate. Now the selective part of the *.parmtop file generated
for my system is given below

%FLAG CHARGE
%FORMAT(5E16.8)
  3.28183623E+00 3.50050383E+00 3.50050383E+00 3.50050383E+00 6.70580640E-01
  2.24316513E+00 -5.15691090E-01 9.38448450E-01 9.38448450E-01 1.06290676E+01
 -1.04668891E+01 -1.57331338E+01 7.46567631E+00 7.46567631E+00 1.12304035E+01
 -1.04268001E+01 -7.05846257E+00 5.47771449E+00 6.82789581E-01 2.77443629E+00
 -5.85154498E-01 5.64800189E-01 5.64800189E-01 -3.69256687E-01 5.61082839E-01
...........

%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ASN GLN ILE ASP LEU ASN VAL THR CYS ARG TYR ALA GLY VAL PHE HIE VAL
GLU LYS ASN ...........

So the N terminal end of the protein is ASN. Now in "all_aminont03.in"
file it is given

ASPARAGINE

 NASN INT 1
 CORR NOMI DU BEG
   0.00000
   1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
   2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
   3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
   4 N N3 M 3 2 1 1.335 116.600 180.000 -0.669106
   5 H1 H E 4 3 2 1.010 130.000 0.000 0.473035
   6 H2 H E 4 3 2 1.010 60.000 90.000 0.473035
   7 H3 H E 4 3 2 1.010 60.000 -90.000 0.473035
   8 CA CT M 4 3 2 1.449 121.900 180.000 0.256684
........................

So for terminal N atom of ASN (in parmtop file) charge =
3.28183623E+00/18.2223 = 0.18009 which is not equal to the value of
-0.669106 given in the above table.

The 2nd res of the protein is GLN. In "all_amino03.in" file it is given that

GLUTAMINE

 GLN INT 1
 CORR OMIT DU BEG
   0.00000
   1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
   2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
   3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
   4 N N M 3 2 1 1.335 116.600 180.000 -0.387353
   5 H H E 4 3 2 1.010 119.800 0.000 0.300605
   6 CA CT M 4 3 2 1.449 121.900 180.000 0.037470
   7 HA H1 E 6 4 3 1.090 109.500 300.000 0.152255
 ......................................

 So for N atom of GLN charge = -7.05846257E+00/18.2223 = -0.38735
which is same as given above in the table.

Thanks,
Madhurima

On Wed, Jul 23, 2008 at 10:46 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> 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
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_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_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu