# [AMBER] pairwise MMPBSA calculations

From: Rana Rehan Khalid via AMBER <amber.ambermd.org>
Date: Fri, 22 Jul 2022 12:42:23 -0400

Dear Amber Users

I am trying to calculate the pairwise energy decomposition using MMPBSA.py.
Total frames I considered for this calculator is 25. my residues mask is

idecomp=3, print_res="29; 31; 33; 37-39; 42; 44; 49; 52; 84; 86; 88; 90;
92-97; 137; 138; 140; 142; 160; 170; 204; 206-213"

This residue mask consists of all interface residues from the receptor and
its cognate. These are total 35 residues.

My question is when I finished calculations each pair of interface residue
printed 35 times with different energy values on which energy value we
need to consider and from where these energy values are coming however I am
consider 25 frames for these calculation, Or maybe I did not set the mask
properly

for exp:

3475 PRO 208 L PRO 99 -1.1942760000000001
3476 PRO 208 L PRO 99 -4.226881
3477 PRO 208 L PRO 99 2.0651900000000003
3478 PRO 208 L PRO 99 1.946714
3479 PRO 208 L PRO 99 -0.977009
3480 PRO 208 L PRO 99 -1.2975789999999998
3481 PRO 208 L PRO 99 70.342555
3482 PRO 208 L PRO 99 -0.5931699999999998
3483 PRO 208 L PRO 99 -95.09110599999998
3484 PRO 208 L PRO 99 6.531091999999999
3485 PRO 208 L PRO 99 0.728705
3486 PRO 208 L PRO 99 -0.4807510000000001
3487 PRO 208 L PRO 99 -4.191134
3488 PRO 208 L PRO 99 -54.34039799999999
3489 PRO 208 L PRO 99 0.8193449999999999
3490 PRO 208 L PRO 99 -0.37730499999999995
3491 PRO 208 L PRO 99 -2.984086000000001
3492 PRO 208 L PRO 99 -0.740205
3493 PRO 208 L PRO 99 0.22672000000000003
3494 PRO 208 L PRO 99 -43.58759500000001
3495 PRO 208 L PRO 99 -4.3538783599999995
3496 PRO 208 L PRO 99 0.11959604000000001
3497 PRO 208 L PRO 99 0.2250334400000007
3498 PRO 208 L PRO 99 -0.1995754799999998
3499 PRO 208 L PRO 99 -0.02986384000000003
3500 PRO 208 L PRO 99 -0.002227360000000001
3501 PRO 208 L PRO 99 0.10555515999999976
3502 PRO 208 L PRO 99 -0.12939263999999995
3503 PRO 208 L PRO 99 -0.26433256000000327
3504 PRO 208 L PRO 99 3.0827192399999976
3505 PRO 208 L PRO 99 -0.25335604000000345
3506 PRO 208 L PRO 99 0.55143716
3507 PRO 208 L PRO 99 -0.12156576
3508 PRO 208 L PRO 99 -0.030905720000000008
3509 PRO 208 L PRO 99 0.01911791999999979

Do I need to get the average of all these 35 times energy values to get
this particular pair of decomposition energy? Please guide

Thanks
Rehan
Postdoctoral Research Associate
Albert Einstein College of Medicine New York
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Received on Thu Aug 04 2022 - 13:35:30 PDT
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