Dear AMBER users,
I am trying to use AMBER Free Energy Workflow (FEW) for my calculation and
for that trying to learn the tutorial (
https://ambermd.org/tutorials/advanced/tutorial24/index.php).
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
(/home/user/tutorial/calc_a_3t/qsub_s51_100_1_pb0_gb2.sh)
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
/usr/local/hpcware/apps/amber/gcc-8.3.1/openmpi-3.1.6-gcc-8.3.1-gpu-10.2/18/AmberTools/src/mm_pbsa/
mm_pbsa_statistics.pm line 957.
shell-init: error retrieving current directory: getcwd: cannot access
parent directories: No such file or directory
gzip:
/home/ykrishnan/work/AMBER/MMPBSA/calc_a_1t/L51c/s81_100_1/pb3_gb0/L51c_statistics.out.gz:
No such file or directory
In the directory i am getting following files as my output
#WORKDIR/calc_a_1t/L51c/s81_100_1/pb3_gb0
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
