From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sat Aug 05 2006 - 16:10:33 CDT
Which ligand are you using with your protein? Psfgen usually outputs
this kind of error when the atom names of your original file (e.g.,
that taken from the PDB or another source) and names of the topology
file(s) you're using. If you're sure that your molecule is already
parametrized (i.e., I've seen the atom type HZ4 for acetone), then
remove the hydrogens from your original file and let psfgen to place
them and guess the coordinates. You can take a look to your topology
file(s) and see if the atoms types match well. It is not very clear
what do you mean when you say that "psfgen does not ask for a topology
file" after adding the atom type HZ4.
You also have to be careful at adding or modifying atoms types to your
already built topologies, because non-adequate changes can potentially
modify your results.
2006/8/5, Dhiraj Srivastava <dhirajks_at_gmail.com>:
> Hi all
> when i am trying to prepare psf file using psfgen for my protein containing
> ligand, i am getting error that atom type HZ4 not found. my topology file
> for ligand has an atom type HZ4. the original parameter file does not have
> atom type HZ4 but i had modified the parameter file so it has atomtype HZ4.
> in psfgen, it never ask for parameter file. so what should i do to resolve
> this problem? why psfgen is showing this error?
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
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