[gmx-users] electron density .dat file

[David van der Spoel]

Jian Dai wrote:
> Hello, all:
> I'm not sure how to make the .dat file in calculating the electron 
> density, for example,
> If I have cholesterol.itp like:
> ;   nr    type   resnr  residu    atom    cgnr    charge   ; total charge
>      1     CH3       1    CHOL     C1        1     0
>      2      CB       1    CHOL     C2         2     0
>      3     CH2       1    CHOL     C3        3     0
>      4     CH2       1    CHOL     C4        4     0
>      5     CH1       1    CHOL     C5        5     0.14 ; charges adopted
>      6      OA       1    CHOL     O6         5     -0.54 ; from Retinol in
>      7      HO       1    CHOL     H          5      0.40 ; ffgmx.rtp
>      ...................................................
> 
> shall I make electron_CHO.dat like:
> 29
> C1 =6
> C2 =6
> C3 =6
> C4 =6
> C5 =6.14
> O6 = 7.46
> H = 1.4
> ....................................
> or like:
> 29
> C1 =6
> C2 =6
> C3 =6
> C4 =6
> C5 = 5.76
> O6 = 8.54
> H =  0.6
> ................................
> 
> I mean, shall I add or subtract the partial charge?
> Thank you in advance and happy Thanksgiving.
> Jian
What do you want to do with this?

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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