Issue Combining PSF and PDB Files

From: Collin Nisler (
Date: Sun Nov 13 2022 - 19:35:31 CST

Hello, I am encountering a strange issue when I try to combine multiple psf an pdb files. I have four chains, each saved as separate psf and pdb files. I have solvated and ionized each chain separately, as a test, and I am able to simulate each separately perfectly fine without issue. When I try combining all into one psf and pdb, either by using the "readpsf" and "coordpdb" command in the tkconsole, the MergeStructs plugin, or by using a psfgen script on just the pdb files, I encounter the "bad global angle" and "bad global dihedral count" errors when I try simulating the complete system. I checked the psf files, and the correct number of angles and dihedrals are present in each case, and there are no obvious issues when I visually inspect the structure. Based on the fact that each runs fine alone, I have to conclude that it is the process of combining all that results in the error, but I am at a complete loss for where the error comes from or even what the source of the error is. Any insight into this issue would be greatly appreciated. Thanks.


This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST