From: Efthymiou, Christos (
Date: Thu Aug 18 2022 - 11:11:35 CDT


I am trying to use the CaFE plugin to calculate the binding free energy of a protein-protein complex, but I get a strange error. The following is printed in the Tk console:

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 14 sec
CaFE) Calculating the MM term
I am not sure what atom type HT1 is, but I have provided the path to all the standard parameter files in my CaFE script such as par_all36_carb.prm, par_all36_cgenff.prm, par_all36_lipid.prm, par_all36_na.prm, par_all36_prot.prm, toppar_all36_carb_glycopeptide.str, and toppar_water_ions_namd.str. My simulation contains two protein chains only with standard amino acids.

In my CaFE script, I provide the path to a psf file containing only the proteins. This psf file was created from the QwikMD generated psf file (generated when preparing the simulation) using the following commands in the Tk console:

set a [atomselect top "protein"]
$a writepsf protein.psf

Here is a comparison of the two psf files:


       1 AP1 0 GLU N NH3 -0.300000 14.0070 0
       2 AP1 0 GLU HT1 HC 0.330000 1.0080 0
       3 AP1 0 GLU HT2 HC 0.330000 1.0080 0
       4 AP1 0 GLU HT3 HC 0.330000 1.0080 0

Protein only PSF:

       1 AP1 0 GLU N N -0.300000 14.0070 0
       2 AP1 0 GLU HT1 HT1 0.330000 1.0080 0
       3 AP1 0 GLU HT2 HT2 0.330000 1.0080 0
       4 AP1 0 GLU HT3 HT3 0.330000 1.0080 0

Therefore, it seems in the protein only psf file the highlighted column has been altered to be identical to the column before it, whereas in the original psf file these two columns are different. Is this the reason for the error? If so, why does the command I used to create the protein psf file cause this to happen?

I cannot use the original psf and dcd file with CaFE as the files are too large and it causes VMD to crash on my Windows 10 computer. I need to be able to use a protein only version of both the psf and dcd files.

I really appreciate any advice on this error.