[AMBER] Confusion of difference EPB value of me and tutorial of MMPBSA.py

From: Dongxiao Yue \(LHS, 220059036\) via AMBER <"Dongxiao>
Date: Sat, 27 Aug 2022 04:03:07 +0000

I used same input prm files as tutorial to repeat the tutorial calculation. the input parameter file is as following:
&general
   endframe=50, keep_files=2,
/
&gb
  igb=2, saltcon=0.100,
/
&pb
  radiopt=0, istrng=0.100, inp=1, cavity_surften=0.00542, cavity_offset=-1.008
/
then I got the following value:

All unit is kcal/mol

            tutorial

            me

GB

PB

GB

PB

VDWAALA

-56.2934

-56.2934

 -56.2921

    -56.2921

EEL

-38.0300

-38.0300

 -38.0301

    -38.0301

EGB/EPB

EGB: 50.2053

EPB: 57.6402

EGB: 50.2050

EPB: 56.8405

DELTA G non-polar

-8.1491

-5.0423

 -8.2682

    -5.0423

DELTA G gas

-94.3234

-94.3234

 -94.3222

    -94.3222

DELTA G solv

42.0562

52.5978

  41.9369

     51.7982

DELTA G binding

-52.2672

-41.7256

 -52.3853

    -42.5240

My EPB value is very different from that of tutorial. I really do not know which parameter can cause their difference. Many years past, mmpbsa.py updated the default parameter and maybe the computational method.
Therefore, can you help me to find the reason causing the different value of me and tutuorail.

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Received on Fri Aug 26 2022 - 21:30:03 PDT
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