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

[Hwankyu Lee]

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?

best,
Hwankyu.


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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