[gmx-users] A question on using g_density for electron densities.
leehk at umich.edu
Mon Mar 1 22:19:01 CET 2004
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
> 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.
> 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
>> 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)
>> 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
>> the atomnames of those residues into electrons.dat by hand?
>> Thanks for your help in advance.
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