Re: NAMD-L: autoionize error

From: Axel Kohlmeyer (
Date: Fri Dec 26 2008 - 14:45:55 CST

On Fri, 26 Dec 2008, wrote:

JG> Dear all,

dear john,

JG> I'm trying to simulate a heteroduplex RNA/DNA system and trying to ionize
JG> to a concentration of 0.1 M. However, I receive this error message upon
JG> the execution of the autoionize script, any suggestions as to the source
JG> of the error?

first of all, please note that this is a VMD question rather
than a NAMD question, so asking on vmd-l might have been
more appropriate.


JG> "autoionize_core -psf C:/Cross Link/rna_autopsf_ws.psf -pdb C:/Cross
JG> Link/rna_autopsf_ws.pdb -o ionized -seg ION -is 0.1 -from 5 -between 5"

your path to the psf and pdb file has blanks in them. this tends to
break a lot of scripts, since they are mostly written on unix/linux
machines, where having blanks in directory or file names is very
uncommon (since they are so inconvenient from the command line).

please try renaming C:/Cross Link to something like C:/Cross_Link
and give it another shot.



JG> John

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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