csu1505110121/pyresp_gen

Incompatibility between espgen output and pyresp_gen.py

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SerpentByte commented
  • Ambertools==23.3

the commands we are using are:

espgen -i run.out -o run.dat -p 1
pyresp_gen.py -i run.dat -f1 1.in -f2 2.in -p chg -q -2

where run.out is the Gaussian (16) log file and run.dat is the esp file generated by espgen.

pyresp_gen.py fails with the following error:
index 0 is out of bounds for axis 0 with size 0

It does not generate 1.in or 2.in. It generated RESPIN1 and RESPIN2. However pyresp.py does not recognize them.
pyresp_files.zip

csu1505110121 commented

Two issues exist:

  1. The file you input are complex instead of single molecule, although pyresp_gen could handle complex molecules. I do not know the purpose of your project. However, you should be careful about this;
  2. When going through your dat file generated by espgen. The element number (4th column, line 2 to 96) are all zero. It looks werid. When I manually corrected them (see attached file), pyresp_gen could run normally. As I mentioned in this tutorial (https://csu1505110121.github.io/tutorial/2023/02/16/pyresp_gen_tutorial.html), latestespgen (at least AMBER 2018) may have some issues, not testing that on Amber 2023 or later version.
    pyresp_files_QZ.zip