Topology files

From: Thomas Kahn (
Date: Fri Feb 12 2010 - 17:13:48 CST

I am trying to build a .psf from 2GOZ.pdb (hammerhead ribozyme), but I keep getting error messages (in VMD/autopsf) about "unparametrized components". After reading into topology files, I now see that the error is due to 4 non-standard nucleotides included in the structure that are not included in my topology file (top_all27_prot_lipid_na.inp). Is there any premade topology file that has an extensive amount of nucleotides? Or even better, is there some sort of database of topology information where I could find entries for the 4 nucleotides and simply add them to the standard file?

Thomas Kahn

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