problems with auto-psf gen and autoionize for ligand with atomtypes of more than 4 characters

From: Raul Araya (
Date: Wed Sep 12 2012 - 16:34:57 CDT

Dear namd users

I'm trying to assemble a system in which a carbohydrate will be considered
as a ligand for a protein. The ligand is being constructed using the latest
charmm force field topology available that includes atom-types of more than
4 characters long. This have caused me many troubles when I try to generate
a correct psf specially when I try to ionize the system with autoionize. I
tried another approach that was to ionize the protein + water system and
then merge that psf/pdb with the psf/pdb from the ligand but it did not
work properly because when I try to run the simulation I got a non-zero
charge for the system. I know there is some issues with the character limit
for the atom-type in the x-plor/NAMD psf files, and I know there is
something about the EXT format for those files but I haven´t got a clear
answer about it from reading the namd or vmd list.


Raúl Araya Secchi
B.Sc Molecular Biotechnology.
Molecular Biotechnology Engineer.
PhD Student (Biotechnology Program. UNAB, Chile)
Computational Biology Lab (DLab)
Center for Mathematical Modeling (CMM)
Facultad de Ciencias Físicas y Matemáticas.
Universidad de Chile.

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