From: Geist, Norman (
Date: Thu Aug 18 2022 - 12:50:18 CDT

Hey, all types are just the atom names. I've seen this happening
when you load the PSF after the PDB before you save the new PSF from
the console. Make sure to always load the PSF first.

Norman Geist

Am Donnerstag, den 18-08-2022 um 18:11 schrieb Efthymiou, Christos:


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
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

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: 

QwikMD PSF: 

       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

I really appreciate any advice on this error.