Dear Amber users,
I am trying to follow the tutorial on free energy calculations using the
FEW tool (
https://ambermd.org/tutorials/advanced/tutorial24/index.php). I have
managed to set up the MD simulations and generate the trajectories.
However, when I try to use LIE.pl to calculate the binding free energies,
the energy estimate is 0.00000 kcal/mol.
I suspect that the error occurs when perl tries to read the sander.out
files. I have compared my sander.out files with those from the tutorial,
and they are similar. However, my ele***.dat and vdw***.dat files are empty
except for the first line *Snapshot EEL 1-4 ELL *or *Snapshot VDW 1-4 VDW*.
When I use perl for the analysis I get the following warnings:
· Odd number of elements in hash assignment at
/work3/heltjo/ComScreen/FEW_Tutorial/LIE.pl line 257.
· Odd number of elements in hash assignment at
/work3/heltjo/ComScreen/FEW_Tutorial/LIE.pl line 258.
· Odd number of elements in hash assignment at
/work3/heltjo/ComScreen/FEW_Tutorial/LIE.pl line 259.
· Odd number of elements in hash assignment at
/work3/heltjo/ComScreen/FEW_Tutorial/LIE.pl line 260.
I am running the simulation with AMBER19 and the calculations with perl
v.5.16.3.
Could you please tell me what can be wrong?
Sincerely,
Helena
*Helena Damtoft Tjørnelund*
PhD student at the Technical University of Denmark
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Received on Tue Mar 02 2021 - 02:30:02 PST
