Dear Jason and Amber Users
In my simulation box I have Urea and Water and now I want to calculate the
average Interaction energy between Urea_Urea, Urea_Water and Water_Water.
For this I process the trajectory to get Average Interaction Energy as
Jason suggested me to used the pairwise command from cpptraj.
By this method I am able to reproduce the average interaction energy of
water_water but fail to reproduce the Average interaction energy between
urea_urea and urea_water.
I given the input for cpptraj.
.........................................................................................................
trajin urea_wat.crd
pairwise U_U :URA out pairwise_uu.dat cuteelec 12.0 cutevdw 12.0
pairwise S_S :SPC out pairwise_ww.dat cuteelec 12.0 cutevdw 12.0
pairwise U_S :URA,SPC out pairwise_us.dat cuteelec 12.0 cutevdw 12.0
...........................................................................................................
The output file for Urea_Urea
..........................................................................................................
#Frame U_U_EVDW U_U_EELEC
1 -155.2368 4250.4339
2 -173.2890 4371.9059
3 -173.9027 4314.2041
4 -175.4758 4346.7265
5 -185.3734 4374.9934
...
...
2495 -191.3443 4315.2169
2496 -167.5771 4325.8357
2497 -163.5134 4351.2010
2498 -179.8482 4369.4136
2499 -169.7458 4278.9632
2500 -166.5782 4314.6092
...............................................................................................................
After switch off the cutoff value and the output value is giving same.
Here I am unable to understand why Urea_Urea Interaction energy have
positive value and vander wall have negative value ?
Does I am doing any here ?
Thank you in advanced
Regard
Rahman
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
On Sun, Apr 6, 2014 at 7:08 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sat, Apr 5, 2014 at 12:05 AM, MOHD HOMAIDUR RAHMAN
> <rahmanhpu.gmail.com>wrote:
>
> > Dear Amber User
> >
> > I want to calculate " Average Interaction Energy " between residues in a
> > simulation box. For this I pack x molecules of A, y molecules of B and z
> > molecules of C in a box. After running MD for few ns now I have crd file.
> >
> > Now from crd I want to calculate the average interaction energy between
> > residue A-A, B-B, C-C, A-B, A-C and B-C.
> >
> > I read about MMPBSA from Amber Tools 12 manual and found that they
> discuss
> > about receptor and ligand only (only two system). While in my case the
> > system is different more than two and with in residue also.
> >
> > Can any one please suggest me to how I will proceed to reach my goal. If
> > any other way to proceed this also welcome.
> >
> > Thank you in advance
> >
>
> Check out the "pairwise" command in cpptraj. It is described in the
> AmberTools 13 manual (p. 253). The usage is:
>
> > help pairwise
> [<name>] [<mask>] [out <filename>] [cuteelec <cute>] [cutevdw <cutv>]
> [ref <reffilename> | refindex <ref#>] [cutout <cutmol2name>]
> Calculate pairwise (non-bonded) energy for atoms in <mask>.
>
> It computes the interaction between all atoms in <mask>. You can do
> something like this:
>
> pairwise aa :A out pairwise.dat cuteelec 12.0 cutevdw 12.0
> pairwise bb :B out pairwise.dat cuteelec 12.0 cutevdw 12.0
> pairwise cc :C out pairwise.dat cuteelec 12.0 cutevdw 12.0
> pairwise ab :A,B out pairwise.dat cuteelec 12.0 cutevdw 12.0
> pairwise ac :A,C out pairwise.dat cuteelec 12.0 cutevdw 12.0
> pairwise bc :B,C out pairwise.dat cuteelec 12.0 cutevdw 12.0
>
> You'll need to process the ab, ac, and bc datasets because they will
> include the homogenous (e.g., A-A, B-B, C-C) as well as the desired
> heterogeneous (e.g., A-B, B-C, A-C) interactions. So you will need to
> subtract out all relevant homogenous interactions (which are calculated in
> the first 3 lines) from the interactions you are computing.
>
> To get the "average" interaction, you will also need to count up how many
> of each species there are and divide by the total number of interactions
> that are occurring based on the simple counting rules.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Wed Apr 16 2014 - 05:30:03 PDT
