Re: PSF files and long atom name

From: Reza (
Date: Mon Jun 10 2013 - 19:45:48 CDT

So I fixed the problem and it turned out to be due to "autoionize" not recognizing the correct PSF type and adding extra ions to the system.

Based on the source code, NAMD 2.9 appears to handle the long atom names correctly and there is no need for adding "NAMD" keyword to the PSF file. However, the "autoionize" plugin in VMD (and in general the PSF reader in VMD) requires this keyword at the beginning of its input PSF file to be able to add the right number of ions.


On Jun 9, 2013, at 3:40 PM, Reza <> wrote:

> Hi all,
> 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?
> Thanks,
> Reza Salari
> 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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