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Electrostatics/apbs
Core Dump (Segmentation Fault) with newer version of APBS

Describe the bug Generating Atom potentials succeeds with APBS Version 1.4.1 but failes (core dump) with version 3.4.1 rubred.pqr.gz test.in.gz To Reproduce Steps to reproduce the behavior: 1. apbs ...
  • srihas29
  • Opened 
    on Aug 9, 2024
  • #293

Electrostatics/apbs
Issue using APBS plugin on polysaccharides

Hi, I am trying to visualize the electrostatic surface of several different kinds of molecules and some of them either contain polysaccharides (for example the protein MUC2, which is often O-glycosylated) ...
  • NoaBinnes
  • 15
  • Opened 
    on Jun 25, 2024
  • #292

Electrostatics/apbs
Ionic Strenght

I want to make APBS calculation for protein-ligand(Calcium ion) in different environmental conditions(physiological and low IS conditions). For physiological condition, I am adding 150mM KCl salts; but ...
  • btayhan
  • Opened 
    on Jun 23, 2024
  • #291

Electrostatics/apbs
Share tool permabug

Describe the bug Error in complied code for 3.4.1 Darwin that I got from releases: share/apbs/tools/manip/inputgen.py To Reproduce Run the setSmallest method of Psize with any input. I don t know where ...
  • EvanKomp
  • 1
  • Opened 
    on May 13, 2024
  • #290

Electrostatics/apbs
Mac Silicon support

Is there a chance to make a release with macOS arm64 binary? I can t seem to make it work. Thank you!
  • kiyoon
  • 10
  • Opened 
    on Mar 21, 2024
  • #289

Electrostatics/apbs
write atompot does not function correctly if the molecule is not the first molecule listed in the input file

Describe the bug After the APBS documentation, I thought that writing out electrostatic potentials at the atom locations should be OK no matter which molecule index (in the READ section) it happens to ...
  • jbardhan
  • 1
  • Opened 
    on Dec 18, 2023
  • #288

Electrostatics/apbs
trying to use apbs with pymol, confused

I m on a mac, 14.1.1, and I m trying to find the charges of a receptor s binding site. I m new to pymol and am not too sure about how to use apbs to visualize it in pymol (following the instructions here: ...
  • ghost
  • 3
  • Opened 
    on Nov 28, 2023
  • #287

Electrostatics/apbs
cmake does not find blas

Hi, I was trying to build APBS (current github repo) from source following the documentation on a machine with openSUSE Tumbleweed. However, cmake (3.27.2) is not able to find the BLAS libraries (see ...
  • vcojocaru
  • 1
  • Opened 
    on Nov 21, 2023
  • #286

Electrostatics/apbs
write statement produces incorrect filenames on linux

Bug: Write statements on linux produce incorrect filenames. It appears that the numerical suffix is being written in a strange (hexidecimal?) floating point format, instead of as an integer. Versions ...
  • fvmarcoline
  • 1
  • Opened 
    on Nov 1, 2023
  • #285

Electrostatics/apbs
Convert DX to Coordinate Plus Scalar Type File

I m trying to transform APBS DX grid to a format that is x,y,z along with the electrostatic potential value. This would be useful for other calculations I want to do. I m attaching a bit of working Python ...
  • sbembenek18
  • 1
  • Opened 
    on Oct 16, 2023
  • #283
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