From: Collin Nisler (cnisler_at_uchicago.edu)
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.
Collin
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