[gmx-users] A question on using g_density for electron densities.
Zhen.Qin at hec.utah.edu
Mon Mar 1 22:28:01 CET 2004
You are welcome. The value is calculated by myself, # of electrons plus
the value of partial charge shown in my lipid.itp file. In the manual of
GROMACS, it is said " the number of electrons for each atom is modified by
its atomic partial charge." So, I added it up. I hope it is correct. :-)
For united atoms or dummy atoms, make sure to take the partial charge into
Have a good day ! ^&^
On Mon, 1 Mar 2004, Hwankyu Lee wrote:
> Thanks for your help. Now I can get electron density profiles, but I'm
> wondering how you get accurate values like you said below. Also, I
> would like to make sure if we don't need to consider H atoms in C1, C2,
> and so forth because of united atoms. Do you have any ideas about
> dummy atoms in proteins like MNZ1, MN1?
> On Mar 1, 2004, at 1:16 PM, Zhen Qin wrote:
> > 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.
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