# pleasa help..SOS

hi
actually this is my assignmnet and what left now is to calculate the free eergy level..
we've been searching for the formula and we couldnt find it~
so, anymone?
plz
this assignment has to be submitted as soon as possible
and i dont know how to do it~
this is the attachment

lina pencilbox

## Comments

• : hi
: actually this is my assignmnet and what left now is to calculate the
: free eergy level..
: we've been searching for the formula and we couldnt find it~
: so, anymone?
: plz
: this assignment has to be submitted as soon as possible
: and i dont know how to do it~
: this is the attachment
:
: lina pencilbox
:
The formula is the sum of the distances between each atom, except for the outer ones. The distance of a single bond is taken as 1. This can easiest be done by numbering the atoms and make an array of each combination of 2 atoms. For the 6 atom molecule as shown in the assignment this array would be:
12, 13, 14, 23, 24, 34
This can be filled using a nested loop (in pseudo code):
[code]
for i = 1 to n-1 {
for j = i+1 to n {
add element ij
}
}
[/code]
for n atoms.
The next step is to determine the spacial location of each atom as described by the input. Since the length of each bond is taken as 1, you can "walk" through the atoms and determine its (x,y) location from the previous one:
[code]
atom[1] = (0,0);
for i = 2 to n {
switch step {
case e: atom[i] = (atom[i-1].x+1,atom[i-1].y)
case n: atom[i] = (atom[i-1].x,atom[i-1].y+1)
case w: atom[i] = (atom[i-1].x-1,atom[i-1].y)
case s: atom[i] = (atom[i-1].x,atom[i-1].y-1)
}
[/code]
Now you can calculate the sum of the distances. For this you'll need the Pythagorean theorem (http://en.wikipedia.org/wiki/Pythagorean_theorem):
[code]
for i = 2 to n {
sum = sum + distance(atom[i-1], atom[i]);
}
[/code]
Then you have calculated the free energy as described just above the "Your Tasks!!" header.
• : : hi
: : actually this is my assignmnet and what left now is to calculate the
: : free eergy level..
: : we've been searching for the formula and we couldnt find it~
: : so, anymone?
: : plz
: : this assignment has to be submitted as soon as possible
: : and i dont know how to do it~
: : this is the attachment
: :
: : lina pencilbox
: :
: The formula is the sum of the distances between each atom, except
: for the outer ones. The distance of a single bond is taken as 1.
: This can easiest be done by numbering the atoms and make an array of
: each combination of 2 atoms. For the 6 atom molecule as shown in
: the assignment this array would be:
: 12, 13, 14, 23, 24, 34
: This can be filled using a nested loop (in pseudo code):
: [code]:
: for i = 1 to n-1 {
: for j = i+1 to n {
: add element ij
: }
: }
: [/code]:
: for n atoms.
: The next step is to determine the spacial location of each atom as
: described by the input. Since the length of each bond is taken as 1,
: you can "walk" through the atoms and determine its (x,y) location
: from the previous one:
: [code]:
: atom[1] = (0,0);
: for i = 2 to n {
: switch step {
: case e: atom[i] = (atom[i-1].x+1,atom[i-1].y)
: case n: atom[i] = (atom[i-1].x,atom[i-1].y+1)
: case w: atom[i] = (atom[i-1].x-1,atom[i-1].y)
: case s: atom[i] = (atom[i-1].x,atom[i-1].y-1)
: }
: [/code]:
: Now you can calculate the sum of the distances. For this you'll need
: the Pythagorean theorem
: (http://en.wikipedia.org/wiki/Pythagorean_theorem):
: [code]:
: for i = 2 to n {
: sum = sum + distance(atom[i-1], atom[i]);
: }
: [/code]:
: Then you have calculated the free energy as described just above the
: "Your Tasks!!" header.

hi..zibadian
first, thnx for helping me
im the beginner in c and i almost have no idea about this assignment
but.i want to ask
is ur formula can be use when the protein shape is changing?
not eenww
..it maybe eennw?
is i applicable?
anyone?
• : : : hi
: : : actually this is my assignmnet and what left now is to calculate the
: : : free eergy level..
: : : we've been searching for the formula and we couldnt find it~
: : : so, anymone?
: : : plz
: : : this assignment has to be submitted as soon as possible
: : : and i dont know how to do it~
: : : this is the attachment
: : :
: : : lina pencilbox
: : :
: : The formula is the sum of the distances between each atom, except
: : for the outer ones. The distance of a single bond is taken as 1.
: : This can easiest be done by numbering the atoms and make an array of
: : each combination of 2 atoms. For the 6 atom molecule as shown in
: : the assignment this array would be:
: : 12, 13, 14, 23, 24, 34
: : This can be filled using a nested loop (in pseudo code):
: : [code]: :
: : for i = 1 to n-1 {
: : for j = i+1 to n {
: : add element ij
: : }
: : }
: : [/code]: :
: : for n atoms.
: : The next step is to determine the spacial location of each atom as
: : described by the input. Since the length of each bond is taken as 1,
: : you can "walk" through the atoms and determine its (x,y) location
: : from the previous one:
: : [code]: :
: : atom[1] = (0,0);
: : for i = 2 to n {
: : switch step {
: : case e: atom[i] = (atom[i-1].x+1,atom[i-1].y)
: : case n: atom[i] = (atom[i-1].x,atom[i-1].y+1)
: : case w: atom[i] = (atom[i-1].x-1,atom[i-1].y)
: : case s: atom[i] = (atom[i-1].x,atom[i-1].y-1)
: : }
: : [/code]: :
: : Now you can calculate the sum of the distances. For this you'll need
: : the Pythagorean theorem
: : (http://en.wikipedia.org/wiki/Pythagorean_theorem):
: : [code]: :
: : for i = 2 to n {
: : sum = sum + distance(atom[i-1], atom[i]);
: : }
: : [/code]: :
: : Then you have calculated the free energy as described just above the
: : "Your Tasks!!" header.
:
: hi..zibadian
: first, thnx for helping me
: im the beginner in c and i almost have no idea about this assignment
: but.i want to ask
: is ur formula can be use when the protein shape is changing?
: not eenww
: ..it maybe eennw?
: is i applicable?
: anyone?
:
The pseudocode I gave can be used with any form or length of protein.
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