[gmx-users] A question on using g_density for electron densities.

[Zhen Qin]

Hi. I used g_density a couple of times. I guess your file format is not
very accurate. This is my file
61
 OW = 7.18
HW1 = 1.41
HW2 = 1.41
 N1 = 6.5
 C2 = 6.4
 C3 = 6.4
 C4 = 6.4
 C5 = 6.3
 C6 = 6.4
 O7 = 7.2
 P8 = 16.7
 O9 = 7.2
O10 = 7.2
O11 = 7.3
C12 = 6.4
C13 = 6.3
O14 = 7.3
C15 = 6.7
.....
C57 = 6
C58 = 6
 It works. You can have a look. Sorry it is a lipid, I donot know the
answer for your 2nd question.

  Good luck.

-Zhen

Have a good day !  ^&^

On Mon, 1 Mar 2004, Hwankyu Lee wrote:

> Dear, gmx-users,
>
> I'm trying to analyze electron density of my systems, but I couldn't
> find enough answers in gromacs homepage. Therefore, I have some
> questions.
>
> 1) When I used -ed option, I got an error like "Fatal error: Invalid
> line in datafile at line 1".
> I made electrons.dat file like below. (let's say that the number of
> atoms are 85)
> --------
> 85
> C1=6
> C2=6
> OW=8
> HW1=1
> HW2=1
> Cl=17
> Na=11
> and so forth......
> --------------
> Is there something wrong with this?  If so, could you show me short
> examples like a simple water box (3atomnames, OW, HW1, and HW2) ??
>
> 2) I'm wondering if I need to write down all the atomnames and # of
> electrons. I'm using 25 residue protein, therefore do I need to put all
> the atomnames of those  residues into electrons.dat by hand?
>
> Thanks for your help in advance.
>
> best,
> Hwankyu.
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>