[gmx-users] charge distribution

[Justin Lemkul]

On 12/29/14 2:31 AM, elham tazikeh wrote:
> Dear Justin
> i really appricite for your help
> i want to tell all did work until now, again:
>
>
> 1.total charges in my topol.top was +2, then by genion, i added 2 CL to  my
> comlex (HSA+Aspirin)
>
> 2.My .itp file (produce by PRODRG) was(consist of 11 atoms) :
>
> [ moleculetype ]
> ; Name nrexcl
> SAL      3
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>       1        OM     1  SAL     O1'     1   -0.765  15.9994 ;'
>       2         C     1  SAL     C1'     1    0.354  12.0110 ;'
>       3        OM     1  SAL     O2'     1   -0.765  15.9994 ;'
>       4         C     1  SAL      C1     1   -0.027  12.0110
>       5       CH2     1  SAL      C6     1    0.102  14.0270
>       6       CH2     1  SAL      C5     1    0.101  14.0270
>       7       CR1     1  SAL      C4     2    0.010  13.0190
>       8       CR1     1  SAL      C3     2    0.010  13.0190
>       9         C     1  SAL      C2     2    0.130  12.0110
>      10        OA     1  SAL      O2     2   -0.191  15.9994
>      11         H     1  SAL      H2     2    0.041   1.0080
>

This explains your previous observations.  This isn't aspirin.  It's salicylic 
acid, albeit incorrect because it has two CH2 groups that should be aromatic. 
It also uses united aromatic carbons, which is incorrect.

>
> with topology file and .itp file, after grompp (for produce nvt.tpr)
> i encounted to below error :
> *system has non-zero total charge : -0.619999*
>

I don't know what could have happened here.  The topology above sums to -1, as 
it should.

>
> 3.as yor re mentioned, Aspirin has 17 atoms.
> for charge distribution, i used of QM (NBO calculation) and my results was:
>      1  C  -0.095205
>      2  C  -0.077566
>      3  C  -0.084684
>      4  C  -0.028579
>      5  C  -0.223106
>      6  C    0.198041
>      7  H    0.147099
>      8  H    0.106100
>      9   H   0.101762
>      10  H  0.117238
>      11  C  0.443312
>      12  O  -0.318010
>      13  H    0.247465
>      14  O  -0.341986
>      15  O  -0.318846
>      16  C    0.312765
>      17  O  -0.320346
>      18  C  -0.281115
>      19  H    0.136126
>      20  H    0.139768
>      21  H    0.139765
>
> these are estimated for* 2-acetoxy benzoic acid *alone (i dont know , must
> be calculate for complex HSA+Aspirin or Aspirin alone?)
>

You can't do the whole complex with QM.  Parametrization would be done on 
aspirin alone, but as I said, you probably don't need to use QM here; you can 
put the topology together from existing building blocks.

> 4. on the other hand, i tried to search in *aminoacids.rtp* file for
> *gromos* force field , but saw only charges for ACE group(other aminoacids
> and some solvents) and i could not find out the charges of all atoms in
> Aspirin molecule.
>

Put it together from building blocks; it's very straightforward.  The aromatic 
ring C-H are the same for PHE and TYR.  The carboxylate is the same for anything 
with an acid (GLU, ASP, C-terminus).  The ester parameters (and likely the C in 
the ring to which it is connected) you have to get from the literature, as this 
functional group is not included in the protein force field.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================