From: Reza (resal81_at_gmail.com)
Date: Sun Jun 09 2013 - 14:40:17 CDT
I have a ligand whose parameters has been generated using CGenff. The ligand has long names for atom types (the longest is 6 characters) and when I run the simulation with NAMD 2.9, it doesn't complain but the total charge is -14 instead of ~0. I'll attach part of the PSF file at the end.
Based on previous posts on the mailing list with similar issues, I added the "NAMD" keyword to the first line of PSF file but I still get -14e total charge. When I looked at the NAMD source code, it seems that NAMD 2.9 uses Molecule.C (instead of molfile_plugin which would recognize the "NAMD" keyword) to parse the PSF file, and by default it expects a space between columns in the atoms section. So the source suggests that if the inter-column space is present, it should be able to handle long names (Molecule.C, lines 1053 and 1094) and I don't understand why it is not the case for my system.
I would appreciate any suggestions about what part I might need to check/change to get the PSF file parsed correctly. Also is there a way to make NAMD to output the results of the PSF parsing, other than modifying and recompiling the source code?
Part of PSF file:
27861 J 348 LIG C0 CG3C52 0.022000 12.0110 0
27862 J 348 LIG C1 CG3RC1 0.026000 12.0110 0
27863 J 348 LIG C2 CG311 0.143000 12.0110 0
27867 J 348 LIG C6 CG2O2 0.900000 12.0110 0
27870 J 348 LIG H1 HGA3 0.090000 1.0080 0
27871 J 348 LIG H2 HGA3 0.090000 1.0080 0
27872 J 348 LIG H3 HGA3 0.090000 1.0080 0
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