From: Qasim Pars (qasimpars_at_gmail.com)
Date: Sat Jul 25 2020 - 23:42:22 CDT
Dear users,
I calculated the hydration free energy of a molecule using NAMD-2.13 with
the thermodynamic integration method. My ti.out file looks like this:
#TITITLE: TS BOND1 AVGBOND1 ELECT1 AVGELECT1
VDW1 AVGVDW1 BOND2 AVGBOND2
ELECT2 AVGELECT2 VDW2 AVGVDW2
#NEW TI WINDOW: LAMBDA 0
#PARTITION 1 SCALING: BOND 1 VDW 0 ELEC 0
#PARTITION 2 SCALING: BOND 1 VDW 1 ELEC 1
#CONSTANT TEMPERATURE: 298.15 K
TI: 0 0.0000 0.0000 -6.1675 -6.1675
-5.5010 -5.5010 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000
TI: 100 0.0000 0.0000 -5.7933 -5.7970
-5.5389 -5.5385 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000
TI: 200 0.0000 0.0000 -3.9530 -4.8796
-5.0426 -5.2918 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000
TI: 300 0.0000 0.0000 1.7023 -2.6929
-4.6941 -5.0932 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000
..
When I run namd2_ti.pl script, I get the below error. Does anyone know how
to fix this error? Or does anyone have another script to calculate the free
energy from the ti.out file of NAMD?
Here is the error after running ./namd2_ti.pl ti.out :
Found 1 output files
Reading files: .Output file ti.out not recognised as a NAMD TI output file
No usable TI output files found - check presence of files in current
directory make sure the correct extension is specified (--extension)
Thanks in advance,
-- Qasim Pars
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