- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Maryam Hamzehee <maryam_h_7860.yahoo.com>

Date: Sun, 2 Jan 2011 20:42:04 +0800 (SGT)

Dear All

I am trying to calculate the binding energy for the complex of ligand-receptor, I have done the MD simulation for a total of 1ns. Then extraction of the snapshots with an interval of 10 ps was performed for the purpose of calculating binding enrgy (total number of 100 snapshots for each of the complex, receptor and ligand).

Consequently, the calculation of binding energy was performed using the following command that I call it method 1:

$AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log

The average of binding energy for the extracted snapshots using PB and GB method was saved in snapshot_statistic.out file.

In the next step I used the following command in order to obtain the average binding energy for restricted the number of snapshots with interval of [snap_min=1, snap_max = 40]. My goal was to obtain the average binding energy for the first 400 ps (method 2).

/home/amber9/src/mm_pbsa/mm_pbsa_statistics.pl 1 0 snapshot_statistics.in test-400ps.out 1 40

My first question: Is this procedure correct for calculation of the first 40 snapshots (first 400 ps)?

I did the same job for snapshots from 1 to 100 (i.e. for all of snapshots) using the following command.

/home/amber9/src/mm_pbsa/mm_pbsa_statistics.pl 1 0 snapshot_statistics.in test-all.out 1 100

I was expecting the value of binding energy (for 1ns using all the snapshots) was the same for method 1 and 2 because in both methods I used all the snapshots for calculating the average binding energy; Surprisingly, I found that the final value of PBTOT (binding free energy using PB method) differs from the one obtained by method 1. But the value of GBTOT was the same for two methods 1 and 2 .I also did the same job for my mutants as well, again the value of PBTOT for all case was different for two methods 1 and 2 and again the value of GBTOT was the same.

My second question: Why the difference between the above mentioned values are observed?

Any help would be highly appreciated.

Cheers,

Maryam

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sun Jan 02 2011 - 05:00:03 PST

Date: Sun, 2 Jan 2011 20:42:04 +0800 (SGT)

Dear All

I am trying to calculate the binding energy for the complex of ligand-receptor, I have done the MD simulation for a total of 1ns. Then extraction of the snapshots with an interval of 10 ps was performed for the purpose of calculating binding enrgy (total number of 100 snapshots for each of the complex, receptor and ligand).

Consequently, the calculation of binding energy was performed using the following command that I call it method 1:

$AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log

The average of binding energy for the extracted snapshots using PB and GB method was saved in snapshot_statistic.out file.

In the next step I used the following command in order to obtain the average binding energy for restricted the number of snapshots with interval of [snap_min=1, snap_max = 40]. My goal was to obtain the average binding energy for the first 400 ps (method 2).

/home/amber9/src/mm_pbsa/mm_pbsa_statistics.pl 1 0 snapshot_statistics.in test-400ps.out 1 40

My first question: Is this procedure correct for calculation of the first 40 snapshots (first 400 ps)?

I did the same job for snapshots from 1 to 100 (i.e. for all of snapshots) using the following command.

/home/amber9/src/mm_pbsa/mm_pbsa_statistics.pl 1 0 snapshot_statistics.in test-all.out 1 100

I was expecting the value of binding energy (for 1ns using all the snapshots) was the same for method 1 and 2 because in both methods I used all the snapshots for calculating the average binding energy; Surprisingly, I found that the final value of PBTOT (binding free energy using PB method) differs from the one obtained by method 1. But the value of GBTOT was the same for two methods 1 and 2 .I also did the same job for my mutants as well, again the value of PBTOT for all case was different for two methods 1 and 2 and again the value of GBTOT was the same.

My second question: Why the difference between the above mentioned values are observed?

Any help would be highly appreciated.

Cheers,

Maryam

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sun Jan 02 2011 - 05:00:03 PST

Custom Search