[gmx-users] the reson for neutralizing the charge

[Justin A. Lemkul]

hazizian wrote:
> Hi
> my ligand is Arginine (so it is not neccessary to use PRODRG )and the OPLS 
> forcefield of gromacs make the itp file of it. I check and all the atoms 
> present in the ligand itp file.There is no missing atom in the file.
> 
>  atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    
> chargeB      massB
>      1   opls_287      1    ARG      N      1       -0.3    14.0067   ; qtot 
> -0.3
>      2   opls_290      1    ARG     H1      1       0.33      1.008   ; qtot 
> 0.03
>      3   opls_290      1    ARG     H2      1       0.33      1.008   ; qtot 
> 0.36
>      4   opls_290      1    ARG     H3      1       0.33      1.008   ; qtot 
> 0.69
>      5   opls_283      1    ARG     CA      1       0.04     12.011   ; qtot 
> 0.73
>      6   opls_140      1    ARG     HA      1       0.06      1.008   ; qtot 
> 0.79
>      7   opls_136      1    ARG     CB      2      -0.12     12.011   ; qtot 
> 0.67
>      8   opls_140      1    ARG    HB1      2       0.06      1.008   ; qtot 
> 0.73
>      9   opls_140      1    ARG    HB2      2       0.06      1.008   ; qtot 
> 0.79
>     10   opls_308      1    ARG     CG      3      -0.05     12.011   ; qtot 
> 0.74
>     11   opls_140      1    ARG    HG1      3       0.06      1.008   ; qtot 
> 0.8
>     12   opls_140      1    ARG    HG2      3       0.06      1.008   ; qtot 
> 0.86
>     13   opls_307      1    ARG     CD      4       0.19     12.011   ; qtot 
> 1.05
>     14   opls_140      1    ARG    HD1      4       0.06      1.008   ; qtot 
> 1.11
>     15   opls_140      1    ARG    HD2      4       0.06      1.008   ; qtot 
> 1.17
>     16   opls_303      1    ARG     NE      5       -0.7    14.0067   ; qtot 
> 0.47
>     17   opls_304      1    ARG     HE      5       0.44      1.008   ; qtot 
> 0.91
>     18   opls_302      1    ARG     CZ      5       0.64     12.011   ; qtot 
> 1.55
>     19   opls_300      1    ARG    NH1      6       -0.8    14.0067   ; qtot 
> 0.75
>     20   opls_301      1    ARG   HH11      6       0.46      1.008   ; qtot 
> 1.21
>     21   opls_301      1    ARG   HH12      6       0.46     1.008   ; qtot 
> 1.67
>     22   opls_300      1    ARG    NH2      7       -0.8    14.0067   ; qtot 
> 0.87
>     23   opls_301      1    ARG   HH21      7       0.46      1.008   ; qtot 
> 1.33
>     24   opls_301      1    ARG   HH22      7       0.46      1.008   ; qtot 
> 1.79
>     25   opls_271      1    ARG      C      8        0.7     12.011   ; qtot 
> 2.49
>     26   opls_272      1    ARG     O1      8       -0.8    15.9994   ; qtot 
> 1.69
>     27   opls_272      1    ARG     O2      8       -0.8    15.9994   ; qtot 
> 0.89
> 
> So for neutralizing I break 0.11 charge to 8 number of 0.01 charge and 6 
> number of 0.005 cherge and add them to 8+3=11 H atoms. so the total charge 
> of my ligand is +1.Is it correct way to solve this problem in the case that 
> I could not find any missing atom in ligand topology file?
> 
> 

No.  When using pdb2gmx, how did you specify the N- and C-termini?  Did you just 
indicate NH3+ and COO-?  If so, this is incorrect.  You have to use the 
zwitterionic options (since you are indeed dealing with a zwitterion).

The broken charge comes from this mistake.

If you ever find yourself with a fractional charge, do not get creative about 
how to interpret it.

-Justin

> Tehran University of Medical Sciences
> www.tums.ac.ir
> 
> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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