error while running browndye2 job

[Pulkit A Sati]

Dear Browndye  developers,

We (myself and @https://github.com/vaibhavadixit) have been attempting to run seekr2 on new systems (after successful training with tutorial).
We closely followed the procedure used for the trypsin-benzamidine system realizing that there ought to be major differences.

Our system is oxygen bound to Heme-Fe, but we parameterized Heme without O2 bound and separately parameterized O2 in G16-antechamber.

In the 1st prepare.py step,  we are getting the following error. regarding failure to generate AssertionError: Problem running make_apbs_input - APBS input files not found: ligand*.in

Browndye and apbs are correctly installed in the seekr environment and are accessible.

cadd-sys3@caddsys3:~/Documents/final_mbo_seekr/seekrtools$ which make_apbs_inputs
/home/cadd-sys3/setupfiles/browndye2/bin/make_apbs_inputs
cadd-sys3@caddsys3:~/Documents/final_mbo_seekr/seekrtools$ apbs --help


----------------------------------------------------------------------
    APBS -- Adaptive Poisson-Boltzmann Solver
    Version 1.5
   
    Nathan A. Baker (nathan...@pnnl.gov)
    Pacific Northwest National Laboratory
   
    Additional contributing authors listed in the code documentation.
   
    Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific
    Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
    Northwest Division for the U.S. Department of Energy.