VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Fri Aug 19 2022 - 04:03:25 CDT

Hello,

I am trying to use the CaFE plugin for VMD on my Windows 10 computer to calculate the free binding energy of a protein-protein complex. I have downloaded and installed the versions mentioned in the manual, including VMD 1.9.2, NAMD 2.9, and Delphi 5.1. The CaFE manual mentions APBS version 1.3, but the oldest version I can find here https://urldefense.com/v3/__https://github.com/Electrostatics/apbs/releases__;!!DZ3fjg!4bW6K2Qk3pWQ7AnA6Gdo1jqKFc-yQC254-lbqefw4u04J_mVL0eThhcaC7bLmi_NIPeHXMFtwjDYftow39HSO1MlDQIScUk$ is 1.4.2.

My CaFE script is:

````
package require cafe 1.0
mmpbsa -top J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/protein.psf \
-trj J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/MD_10stride_protein.dcd \
-out mmpbsa.log \
-par J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/par_all36_carb.prm \
-par J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/par_all36_cgenff.prm \
-par J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/par_all36_lipid.prm \
-par J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/par_all36_na.prm \
-par J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/par_all36_prot.prm \
-par J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/toppar_all36_carb_glycopeptide.str \
-par J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/3OXU_Starting_Structure/Wildtype/Wildtype_20ns_Test1/Wildtype_20ns_Test1/run/toppar_water_ions_namd.str \
-com "segname AP1 EP1" \
-rec "segname AP1" \
-lig "segname EP1" \
-first 0 \
-last -1 \
-stride 100 \
-mm 1 \
-mm_exe C:/Users/Christos/Documents/CaFE_Executables/NAMD_2.9_Win64-MPI/NAMD_2.9_Win64-MPI/namd2.exe \
-pb 1 \
-pb_exe C:/Users/Christos/Documents/CaFE_Executables/DelPhi_WIN_F77/DelPhi_WIN_F77/executable/delphi77.exe \
-pb_rad mparse \
-sa 1 \
-sa_rad mparse \
-sa_gamma 0.00542 \
-sa_beta 0.92
quit
````
When I run this script, I see this:
````
CaFE) Sanity check
CaFE) Found 6623 atoms for complex
CaFE) Found 4669 atoms for receptor
CaFE) Found 1954 atoms for ligand
CaFE) Loaded 1001 frames for complex
CaFE) Generating new trajectory for complex
CaFE) Loaded 11 frames for complex
CaFE) It took 0 days 0 hrs 0 min 26 sec
CaFE) Calculating the MM term
CaFE) It took 0 days 0 hrs 0 min 19 sec
CaFE) Calculating the PB term
CaFE) Error: Unknown or broken DelPhi output file: com_pb_tmp_0.log
````

If I try to use APBS instead, when it gets to "Calculating the PB term", the program stalls and then an error from Microsoft Visual C++ Runtime Library appears on the screen:

````
Debug error!
Program: C:\APBS\apbs.exe
abort() has been called
(Press Retry to debug the application)
````
If I press Retry, that error message disappears and the Tk console then prints

````
child killed: trace trap
````

If I try to run APBS independently outside of VMD/CaFE, it opens a terminal and seems to have been installed correctly.

Any advice on how to solve these errors is greatly appreciated as I cannot find any information online.