From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Jul 06 2008 - 22:06:53 CDT

Hi Paul,

Paul Dennis Simonson wrote:
> I am interested in doing a simple equilibration on my protein (3KIN).
> I am trying to use the autopsf plugin, and I run into two problems:
> 1. I am trying to patch two segments together, but I do not know
> what kind of patch to apply. Basically, the protein is dimeric, but
> there are four auto-generated segments. I want to patch (twice) the
> end of one segment to the beginning of the next one so that I end up
> with 2 protein segments. How do I do it?

Are you sure you want to make your protein into only two covalently
bonded chains? If autopsf separated them, either the chains have
different chain names in the pdb or there's a large gap in residue
numbering. If this is really what you want you should just delete the
four autogenerated protein chains and then use the "Add a new chain"
button to add segments covering the parts of the protein you want.
> 2. When I ignore the patching issue and just go with the automated
> output, and I choose "Solvate" and "Ionize", it seems to produce the
> output files okay, but the program hangs. I am running VMD 1.86 on an
> Intel Mac running OS 10.5.3. I end up having to close VMD by closing
> the terminal window.
>
> Taking my autopsf files, I then try to run a namd simulation
> (basically a modified version of the water box equilibration of
> ubiquitin from the tutorials), but I get the following error message:
> "------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CN7
>
> Charm++ fatal error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CN7
You need to use a parameter file suitable for nucleic acids, such as
par_all27_na.inp or par_all27_prot_na.inp (note the na in the file
name). You should be able to get them from the MacKerell lab website,
among other places.

Best,
Peter