[AMBER] MMPBSA calculation error

From: Yogeshwaran Krishnan <yogeshwaran.krishnan.ucdconnect.ie>
Date: Tue, 4 May 2021 13:09:25 +0100

Dear AMBER users,

I am trying to use AMBER Free Energy Workflow (FEW) for my calculation and
for that trying to learn the tutorial (

I can do the following steps
A: Preparation of parameter files
B: Preparation of MD input files
A: 1(3)-trajectory approach
$FEW/FEW.pl MMPBSA /home/user/tutorial/cfiles/mmpbsa_am1_1trj_pb3_gb0
I was successful on these steps.

However, In the next step
I am getting following error

=>> Calculating energy / entropy contributions

=>> Doing statistics
=>> Reading input
=>> Reordering files
    Final order:
    1. L51c_com.all.out: -
    2. L51c_rec.all.out: -
    3. L51c_lig.all.out: -
=>> Reading files
    Reading L51c_com.all.out
    Reading L51c_rec.all.out
    Reading L51c_lig.all.out
=>> Values of parameters
    TEMP = 300
    R = 8.314
    gammaP = 0.00542
    betaP = 0.92
    gammaG = 0.0072
    betaG = 0.00
=>> Treat special parameters
=>> Calc missing parameters
    Processing MM GAS
    Processing MM INT
    Processing MM ELE
    Processing MM VDW
    Processing PB PBSOL
    Processing PB PBELE
    Processing PB PBTOT
=>> Calc delta from raw data
Can't use an undefined value as an ARRAY reference at
mm_pbsa_statistics.pm line 957.
shell-init: error retrieving current directory: getcwd: cannot access
parent directories: No such file or directory
No such file or directory

In the directory i am getting following files as my output
L51c_com.all.out.gz L51c_lig.all.out.gz L51c_rec.all.out.gz
 L51c_statistics.in.gz mmpbsa.in run_mmpbsa.pbs

Please let me know where I am making mistakes.

Thank you in advance
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Received on Tue May 04 2021 - 05:30:03 PDT
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